App.R

######## PhyloTrace #########

options(ignore.negative.edge = TRUE)
options(shiny.error = browser)
Sys.setlocale("LC_TIME", "C")

# _______________________ ####
# CRAN Packages
library(shiny)
library(R.utils)
library(igraph)
library(ComplexHeatmap)
library(shinyWidgets)
library(shinydashboard)
library(dashboardthemes)
library(ggplot2)
library(ggnewscale)
library(ggplotify)
library(grid)
library(gridExtra)
library(ape)
library(tidyverse)
library(rlang)
library(tidytree)
library(shinyFiles)
library(dplyr)
library(downloader)
library(rvest)
library(rmarkdown)
library(knitr)
library(kableExtra)
library(fs)
library(data.table)
library(zoo)
library(ggnetwork)
library(rhandsontable)
library(visNetwork)
library(proxy)
library(phangorn)
library(cowplot)
library(waiter)
library(viridis)
library(RColorBrewer)
library(bslib)
library(bsicons)
library(DT)
library(shinyBS)
library(openssl)
library(logr)
# Bioconductor Packages
library(treeio)
library(ggtree)
library(ggtreeExtra)

source("./assets/constants.R")
source("./assets/functions.R")
source("./assets/ui_modules.R")

# User Interface ----

ui <- dashboardPage(
  title = "PhyloTrace 1.6.0",
  
  # Title
  dashboardHeader(
    title = span(
      div(
        class = "img_logo",
        a(
          href = "https://www.liora-bioinformatics.com/phylotrace",  
          target = "_blank",                     
          img(
            src = "PhyloTrace_BW.png", width = 190
          )
        )
      )
    ),
    uiOutput("loaded_scheme"),
    uiOutput("statustext"),
    uiOutput("databasetext"),
    dropdownMenuOutput("notificationMenu"),
    tags$li(
      class = "dropdown",
      fluidRow(
        actionBttn(
          "support_menu",
          label = "",
          color = "default",
          size = "sm",
          style = "material-flat",
          icon = icon("circle-question")
        )
      )
    ),
    tags$li(
      class = "dropdown",
      fluidRow(
        actionBttn(
          "settings_menu",
          label = "",
          color = "default",
          size = "sm",
          style = "material-flat",
          icon = icon("gear")
        )
      )
    ),
    tags$li(
      class = "dropdown",
      fluidRow(
        actionBttn(
          "shutdown",
          label = "",
          color = "default",
          size = "sm",
          style = "material-flat",
          icon = icon("xmark")
        )
      )
    ),
    tags$li(class = "dropdown", 
            tags$span(id = "currentTime", style = "color:black; font-weight:bold;")),
    disable = FALSE
  ),
  
  ## Sidebar ----
  dashboardSidebar(
    tags$head(includeCSS("www/head.css")),
    tags$style(includeCSS("www/body.css")),
    tags$style(HTML(
      "@keyframes pulsate {
       0% { transform: scale(1); }
        50% { transform: scale(1.1); }
        100% { transform: scale(1); }
       }
       .pulsating-button {
        animation: pulsate 1s ease infinite;
        width: 40px !important;
       }
       .pulsating-button:hover {
        animation: none;
       }
      ")),
    br(),
    sidebarMenu(
      id = "tabs",
      br(), 
      uiOutput("menu_header_typing"),
      br(),
      sidebarMenuOutput("menu_typing"),
      br(), br(), 
      uiOutput("menu_header_screening"),
      br(), 
      sidebarMenuOutput("menu_screening")
    )
  ),
  
  dashboardBody(
    div(id = "blocking-overlay"),
    tags$head(tags$link(rel = "shortcut icon", href = "pt_small_icon.png")),
    shinyjs::useShinyjs(),
    shinyDashboardThemeDIY(
      ### general
      appFontFamily = "Liberation Sans",
      appFontColor = "#000000",
      primaryFontColor = "#ffffff",
      infoFontColor = "rgb(0,0,0)",
      successFontColor = "rgb(0,0,0)",
      warningFontColor = "rgb(0,0,0)",
      dangerFontColor = "rgb(0,0,0)",
      bodyBackColor = cssGradientThreeColors(
        direction = "down",
        colorStart = "#282f38",
        colorMiddle = "#384454",
        colorEnd = "#495d78",
        colorStartPos = 0,
        colorMiddlePos = 50,
        colorEndPos = 100
      ),
      
      ### header
      logoBackColor = "#282f38",
      headerButtonBackColor = "#282f38",
      headerButtonIconColor = "#18ece1",
      headerButtonBackColorHover = "#282f38",
      headerButtonIconColorHover = "#ffffff",
      headerBackColor = "#282f38",
      headerBoxShadowColor = "#aaaaaa",
      headerBoxShadowSize = "0px 0px 0px",
      
      ### sidebar
      sidebarBackColor = cssGradientThreeColors(
        direction = "down",
        colorStart = "#282f38",
        colorMiddle = "#384454",
        colorEnd = "#495d78",
        colorStartPos = 0,
        colorMiddlePos = 50,
        colorEndPos = 100),
      
      sidebarPadding = 0,
      sidebarMenuBackColor = "transparent",
      sidebarMenuPadding = 0,
      sidebarMenuBorderRadius = 0,
      sidebarShadowRadius = "5px 5px 5px",
      sidebarShadowColor = "#282f38",
      sidebarUserTextColor = "#ffffff",
      sidebarSearchBackColor = "rgb(55,72,80)",
      sidebarSearchIconColor = "rgb(153,153,153)",
      sidebarSearchBorderColor = "rgb(55,72,80)",
      sidebarTabTextColor = "rgb(255,255,255)",
      sidebarTabTextSize = 15,
      sidebarTabBorderStyle = "none none solid none",
      sidebarTabBorderColor = "rgb(35,106,135)",
      sidebarTabBorderWidth = 0,
      sidebarTabBackColorSelected = cssGradientThreeColors(
        direction = "right",
        colorStart = "rgba(44,222,235,1)",
        colorMiddle = "rgba(44,222,235,1)",
        colorEnd = "rgba(0,255,213,1)",
        colorStartPos = 0,
        colorMiddlePos = 30,
        colorEndPos = 100
      ),
      sidebarTabTextColorSelected = "rgb(0,0,0)",
      sidebarTabRadiusSelected = "0px 0px 0px 0px",
      sidebarTabBackColorHover = cssGradientThreeColors(
        direction = "right",
        colorStart = "rgba(44,222,235,1)",
        colorMiddle = "rgba(44,222,235,1)",
        colorEnd = "rgba(0,255,213,1)",
        colorStartPos = 0,
        colorMiddlePos = 30,
        colorEndPos = 100
      ),
      sidebarTabTextColorHover = "rgb(50,50,50)",
      sidebarTabBorderStyleHover = "none none solid none",
      sidebarTabBorderColorHover = "rgb(75,126,151)",
      sidebarTabBorderWidthHover = 0,
      sidebarTabRadiusHover = "0px 0px 0px 0px",
      
      ### boxes
      boxBackColor = "#ffffff",
      boxBorderRadius = 7,
      boxShadowSize = "0px 0px 0px",
      boxShadowColor = "#ffffff",
      boxTitleSize = 20,
      boxDefaultColor = "#00a65a",
      boxPrimaryColor = "#ffffff",
      boxInfoColor = "#00a65a",
      boxSuccessColor = "#00a65a",
      boxWarningColor = "#ffffff",
      boxDangerColor = "#ffffff",
      tabBoxTabColor = "#ffffff",
      tabBoxTabTextSize = 14,
      tabBoxTabTextColor = "rgb(0,0,0)",
      tabBoxTabTextColorSelected = "rgb(0,0,0)",
      tabBoxBackColor = "#ffffff",
      tabBoxHighlightColor = "#ffffff",
      tabBoxBorderRadius = 5,
      
      ### inputs
      buttonBackColor = "#282F38",
      buttonTextColor = "#ffffff",
      buttonBorderColor = "#282F38",
      buttonBorderRadius = 5,
      buttonBackColorHover = cssGradientThreeColors(
        direction = "right",
        colorStart = "rgba(44,222,235,1)",
        colorMiddle = "rgba(44,222,235,1)",
        colorEnd = "rgba(0,255,213,1)",
        colorStartPos = 0,
        colorMiddlePos = 30,
        colorEndPos = 100
      ),
      buttonTextColorHover = "#000000",
      buttonBorderColorHover = "transparent",
      textboxBackColor = "#ffffff",
      textboxBorderColor = "#ffffff",
      textboxBorderRadius = 5,
      textboxBackColorSelect = "#ffffff",
      textboxBorderColorSelect = "#000000",
      
      ### tables
      tableBackColor = "rgb(255,255,255)",
      tableBorderColor = "rgb(240,240,240)",
      tableBorderTopSize = 1,
      tableBorderRowSize = 1
    ),
    
    uiOutput("start_message"),
    
    tabItems(
      
      ## Tab Database ----
      
      ### Tab Browse Entries ----
      
      tabItem(
        tabName = "db_browse_entries",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Browse Entries"), style = "color:white")
          ),
          column(
            width = 7,
            align = "left",
            p(
              HTML(
                paste0(
                  '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                  'Browse and manage the local database with entries comprising isolates with their metadata, variables and results of cgMLST Typing.',
                  '</span>'
                )
              )
            )
          )
        ),
        hr(), br(), 
        fluidRow(
          column(1),
          div(
            class = "db-table-column",
            column(
              width = 8,
              fluidRow(
                column(
                  width = 12,
                  uiOutput("no_scheme_entries"),
                  uiOutput("db_no_entries"),
                  uiOutput("entry_table_controls")
                )
              ),
              fluidRow(
                div(
                  class = "db-table-column",
                  column(
                    width = 12,
                    br(),
                    uiOutput("db_entries_table")
                  )  
                )
              )
            )
          ),
          div(
            class = "db-controls-column",
            column(
              width = 3,
              align = "left",
              uiOutput("custom_var_box"),
              uiOutput("delete_box"),
              uiOutput("compare_allele_box"),
              uiOutput("download_entries")
            )
          )
        )
      ),
      
      ### Tab Scheme Info  ----  
      
      tabItem(
        tabName = "db_schemeinfo",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Scheme Info"), style = "color:white")
          ),
          column(
            width = 1,
            align = "left",
            uiOutput("download_scheme_info")
          ),
          column(
            width = 7,
            align = "left",
            p(
              HTML(
                paste0(
                  '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                  'Information about the currently selected scheme and the respective species.',
                  '</span>'
                )
              )
            )
          )
        ),
        hr(), br(), 
        uiOutput("no_scheme_info"),
        fluidRow(
          column(1),
          column(
            width = 5,
            tableOutput("scheme_info")
          ),
          column(
            width = 5,
            uiOutput("species_info_select_saved"),
            uiOutput("species_info_saved")
          )
        )
      ),
      
      ### Tab Loci Info  ----  
      
      tabItem(
        tabName = "db_loci_info",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Loci Info"), style = "color:white")
          ),
          column(
            width = 1,
            uiOutput("download_loci")
          ),
          column(
            width = 7,
            align = "left",
            uiOutput("loci_info_text"),
            uiOutput("db_loci_no")
          )
        ),
        hr(), 
        fluidRow(
          column(1),
          div(
            class = "loci-info-column",
            column(
              width = 7,
              align = "center",
              br(),
              div(class = "loci_table",
                  dataTableOutput("db_loci"))
            )
          ),
          div(
            class = "loci-controls-column",
            column(
              width = 4,
              br(),
              uiOutput("sequence_selector"),
              uiOutput("loci_sequences")
            )
          )
        )
      ),
      
      ### Tab Distance Matrix  ----  
      
      tabItem(
        tabName = "db_distmatrix",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Distance Matrix"), style = "color:white")
          ),
          uiOutput("distance_matrix_info")
        ),
        hr(),
        br(),
        uiOutput("no_scheme_distancematrix"),
        uiOutput("distancematrix_no_entries"),
        uiOutput("distmatrix_show"),
        br()
      ),
      
      ### Tab Missing Values ----
      
      tabItem(
        tabName = "db_missing_values",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Missing Values"), style = "color:white")
          ),
          column(
            width = 1,
            align = "left",
            downloadBttn(
              "download_na_matrix",
              style = "simple",
              label = "",
              size = "sm",
              icon = icon("download")
            )
          ),
          column(
            width = 7,
            align = "left",
            p(
              HTML(
                paste0(
                  '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                  "Overview of isolates whose allelic profile contains missing values (NA). This occurs if no allele could be assigned for a locus.",
                  '</span>'
                )
              )
            )
          )
        ),
        hr(), br(), 
        fluidRow(
          column(1),
          div(
            class = "miss-val-column",
            column(
              width = 3,
              uiOutput("missing_values")
            )
          ),
          div(
            class = "miss-val-table-col",
            column(
              width = 7,
              rHandsontableOutput("table_missing_values"),
              br(),
              fluidRow(
                column(
                  width = 2,
                  div(
                    class = "rectangle-red-space" 
                  )
                ),
                column(
                  width = 10,
                  align = "left",
                  p(
                    HTML(
                      paste(
                        tags$span(style="color: white; font-size: 15px; position: relative; bottom: -12px", "≥ 5% of loci missing")
                      )
                    )
                  )
                )
              )
            )
          )
        )
      ),
      
      ## Tab Manage Schemes  ----  
      
      tabItem(
        tabName = "init",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Manage Schemes"), style = "color:white")
          ),
          column(
            width = 7,
            align = "left",
            p(
              HTML(
                paste0(
                  '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                  'Browse remote cgMLST schemes available on ',
                  ' <a href="', 'https://www.cgmlst.org/ncs/' , '" target="_blank" style="color:#008edb; text-decoration:none;"> cgMLST.org Nomenclature Server (h25) </a>',
                  ' and ',
                  ' <a href="', 'https://pubmlst.org/' , '" target="_blank" style="color:#008edb; text-decoration:none;"> pubMLST </a>',
                  ' databases.',
                  '</span>'
                )
              )
            )
          )
        ),
        hr(), br(),
        fluidRow(
          column(1),
          column(
            width = 5,
            div(
              class = "scheme-sel-box",
              box(
                solidHeader = TRUE,
                status = "primary",
                width = "100%",
                title = "Scheme Selection",
                fluidRow(
                  column(
                    width = 4,
                    p(
                      HTML(
                        paste0(
                          '<span style="color: white; font-size: 15px; position:relative; top: 15px; left: 30px;">', 
                          '<i class="fas fa-layer-group" style="color:white; font-size: 15px"></i>',
                          'Select Scheme'
                        )
                      )
                    )
                  ),
                  column(
                    width = 8,
                    align = "left",
                    uiOutput("scheme_selector")
                  )
                )
              )
            )
          ),
          column(1),
          column(
            width = 5,
            div(
              class = "manage-schemes-actions-box",
              box(
                solidHeader = TRUE,
                status = "primary",
                width = "100%",
                title = "Fetch Data from Scheme Database",
                fluidRow(
                  column(1),
                  column(
                    width = 5,
                    shinyjs::disabled(
                      actionButton(
                        "download_cgMLST",
                        label = "Download",
                        icon = icon("download")
                      )
                    ),
                    shinyjs::hidden(
                      div(
                        id = "downloading",
                        HTML(
                          paste0(
                            "<span style='color: white; font-size: 15px; position: relative;top: 5px;'>", 
                            "Downloading scheme",
                            '<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white; margin-left: 15px; position: relative; top: 6px; margin-bottom: 26px;"></i>'
                          )
                        )
                      )
                    ),
                    shinyjs::hidden(
                      div(
                        id = "hashing",
                        HTML(
                          paste0(
                            "<span style='color: white; font-size: 15px; position: relative;top: 5px;'>", 
                            "Hashing scheme",
                            '<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white; margin-left: 15px; position: relative; top: 6px; margin-bottom: 26px;"></i>'
                          )
                        )
                      )
                    )
                  ),
                  column(
                    width = 6,
                    uiOutput("scheme_update_info")
                  )
                )
              )
            )
          )
        ),
        br(),
        fluidRow(
          column(1),
          column(
            width = 5,
            align = "left",
            uiOutput("cgmlst_scheme_table")
          ),
          column(
            width = 5,
            uiOutput("species_info_select"),
            uiOutput("species_info")
          )
        )
      ),
      
      
      
      ## Tab Allelic Typing ----------------------------------------------
      
      
      tabItem(
        tabName = "typing",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Generate Allelic Profile"), style = "color:white")
          )
        ),
        hr(),
        uiOutput("typing_no_db"),
        fluidRow(
          uiOutput("initiate_multi_typing_ui"),
          uiOutput("multi_stop"),
          column(1),
          uiOutput("start_multi_typing_ui")
        ),
        fluidRow(
          column(
            width = 6,
            uiOutput("pending_typing")
          ),
          column(
            width = 6,
            uiOutput("multi_typing_results")
          )
        )
      ),
      
      
      ## Tab Visualization -------------------------------------------------------
      
      
      tabItem(
        tabName = "visualization",
        fluidRow(
          column(
            width = 5,
            br(),
            div(
              class = "vis-control-box",
              uiOutput("generate_plot_ui")
            )
          ),
          column(
            width = 7,
            br(),
            conditionalPanel(
              "input.tree_type=='MST'",
              div(
                class = "vis-control-box-2",
                mst_control_box
              )
            ),
            conditionalPanel(
              "input.tree_type=='Tree'",
              div(
                class = "vis-control-box-2",
                nj_control_box
              )
            )
          )
        ),
        fluidRow(
          tags$script(src = "javascript_functions.js"),
          column(
            width = 2,
            conditionalPanel(
              "input.tree_type=='MST'",
              div(
                class = "vis-control-box-3",
                uiOutput("mst_controls")
              )
            ),
            conditionalPanel(
              "input.tree_type=='Tree'",
              div(
                class = "vis-control-box-3",
                uiOutput("tree_controls")
              )
            )
          ),
          column(
            width = 9,
            align = "left",
            br(),
            conditionalPanel(
              "input.tree_type=='MST'",
              uiOutput("mst_field")
            ),
            conditionalPanel(
              "input.tree_type=='Tree'",
              uiOutput("tree_field")
            )
          )
        )
      ),
      
      ## Tab Screening -------------------------------------------------------
      
      tabItem(
        tabName = "gs_screening",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
          ),
          column(
            width = 7,
            align = "left",
            uiOutput("gene_screening_info")
          )
        ),
        br(),
        hr(),
        fluidRow(
          uiOutput("screening_interface")
        )
      ),
      
      ## Tab Resistance Profile -------------------------------------------------------
      
      tabItem(
        tabName = "gs_profile",
        fluidRow(
          column(
            width = 3,
            align = "center",
            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
          ),
          column(
            width = 7,
            align = "left",
            uiOutput("gene_resistance_info")
          )
        ),
        br(),
        hr(),
        br(), br(),
        fluidRow(
          column(1),
          uiOutput("gs_profile_display")
        )
      ),
      
      ## Tab GS Visualization -------------------------------------------------------
      
      tabItem(
        tabName = "gs_visualization",
        uiOutput("gs_visualization_ui")
      )
    ) # End tabItems
  ) # End dashboardPage
) # end UI

# _______________________ ####

# Server ----

server <- function(input, output, session) {
  
  ## Reactives ----
  
  # default plot control input values
  
  fruit_width <- reactive({
    if(!is.null(nj_layout_val())) {
      if(!is.null(Vis$nj_min_x) & !is.null(Vis$nj_max_x)) {
        if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
          ifelse(nj_layout_val() == "circular" | 
                   nj_layout_val() == "inward",
                 width <- 3,
                 width <- 1) 
        } else {
          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
          if(nj_layout_val() == "circular" | 
             nj_layout_val() == "inward") {
            width <- width * 3
          }
          if(width < 1) {width <- 1}
        }
      } else {
        ifelse(nj_layout_val() == "circular" | 
                 nj_layout_val() == "inward",
               width <- 3,
               width <- 1) 
      } 
    } else {width <- 1}
    
    return(width)
  })
  
  heatmap_width <- reactive({
    if(!is.null(nj_layout_val())) {
      if(!is.null(nj_heatmap_select_val())) {
        length_input <- length(nj_heatmap_select_val())
        if(nj_layout_val() != "circular" & 
           nj_layout_val() != "inward") {
          if(length_input < 3) {
            width <- 0.1
          } else {
            if (length_input >= 3 && length_input <= 50) {
              width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
            } else {
              width <- 1.5
            }   
          }
        } else {
          if(length_input < 3) {
            width <- 0.3
          } else if (length_input >= 3 && length_input <= 27) {
            width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
          } else {
            width <- 3
          }
        }
      } else {width <- 0.1}
    } else {width <- 0.1}
    
    return(width)
  })
  
  clade_highlight_color <- reactive({
    
    selected_nodes <- nj_parentnode_val()
    if (length(selected_nodes) == 1 && selected_nodes == "") selected_nodes <- NULL
    
    if(length(selected_nodes) > 0) {
      if(length(selected_nodes) == 1) {
        if(!is.null(nj_clade_scale_val())) {
          if(!startsWith(nj_clade_scale_val(), "#")) {
            "#D0F221"
          } else {
            nj_clade_scale_val()
          }
        } else {
          "#D0F221"
        }
      } else {"Set1"}
    } else {"#D0F221"}
  })
  
  nj_tippoint_scale_val_default <- reactive({
    determine_scale(
      variable_val = nj_tipcolor_mapping_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Set1"
    )
  })
  
  nj_tiplab_scale_val_default <- reactive({
    determine_scale(
      variable_val = nj_color_mapping_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Set1"
    )
  })
  
  nj_tiles_scale_1_val_default <- reactive({
    determine_scale(
      variable_val = nj_fruit_variable_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Accent"
    )
  })
  
  nj_tiles_scale_2_val_default <- reactive({
    determine_scale(
      variable_val = nj_fruit_variable_2_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Accent"
    )
  })
  
  nj_tiles_scale_3_val_default <- reactive({
    determine_scale(
      variable_val = nj_fruit_variable_3_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Accent"
    )
  })
  
  nj_tiles_scale_4_val_default <- reactive({
    determine_scale(
      variable_val = nj_fruit_variable_4_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Accent"
    )
  })
  
  nj_tiles_scale_5_val_default <- reactive({
    determine_scale(
      variable_val = nj_fruit_variable_5_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Accent"
    )
  })
  
  nj_heatmap_scale_val_default <- reactive({
    determine_scale(
      variable_val = nj_heatmap_select_val(),
      meta_nj = Vis$meta_nj,
      numeric_scale = "viridis",
      long_scale = "turbo",
      short_scale = "Dark2"
    )
  })
  
  # Change UI values reactively

  tree.type.info <- reactive({
    mst_text <- paste(
      "A minimum-spanning tree (MST) connects samples using",
      "the shortest total genetic distances without assuming",
      "an evolutionary model, making it ideal for visualizing",
      "practical relationships, such as population structure",
      "or transmission pathways. It prioritizes simplicity and",
      "may not reflect ancestry or divergence patterns.",
      sep = " "
    )
    tree_text <- paste(
      "A hierarchical tree assumes evolutionary relationships and organizes samples",
      "into a bifurcating structure, illustrating divergence from common ancestors.",
      "It is better suited for visualizing broader evolutionary trends but relies",
      "on model assumptions that may oversimplify local genetic relationships.",
      sep = " "
    )
    if(!is.null(input$tree_type)) {
      if(input$tree_type == "MST") {
        mst_text
      } else {
        tree_text
      } 
    } else {
      mst_text
    }
  })
  
  # tree.type.title <- reactive({
  #   if(input$tree_type == "MST") {
  #     "Minimum-Spanning Tree"
  #   } else {
  #     paste(
  #       "A hierarchical tree assumes evolutionary relationships and organizes samples",
  #       "into a bifurcating structure, illustrating divergence from common ancestors.",
  #       "It is better suited for visualizing broader evolutionary trends but relies",
  #       "on model assumptions that may oversimplify local genetic relationships.",
  #       sep = " "
  #     )
  #   }
  # })
  # 
  
  plot.control <- reactive({
    if(!is.null(input$tree_type)) {
      if(input$tree_type == "MST") {
        "Generate Minimum-Spanning Tree"
      } else {
        "Generate Hierarchical Tree"
      }
    } else {
      "Generate Minimum-Spanning Tree"
    }
  })
  
  # Get rhandsontable
  get.entry.table.meta <- reactive({
    if(!is.null(hot_to_r(input$db_entries))){
      table <- hot_to_r(input$db_entries)
      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
    }
  })
  
  entry_table_height <- reactive({
    if(!is.null(DB$data)) {
      if(nrow(DB$data) > 24){
        height <- 600
      } else {
        height <- NULL
      }
    } else {
      height <- NULL
    }
  })
  
  # Function to check for duplicate isolate IDs for multi typing start
  dupl_mult_id <- reactive({
    req(Typing$multi_sel_table)
    if(!is.null(DB$data)) {
      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
      selection$Files
    } else {""}
  })
  
  # Function to check single typing log file
  check_new_entry <- reactive({
    
    invalidateLater(5000, session)
    
    if(!is.null(Startup$database) & !is.null(DB$scheme)) {
      if(file_exists(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
        
        Database <- readRDS(file.path(Startup$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
        
        if(is.null(DB$data)) {
          if(nrow(Database[["Typing"]]) >= 1) {
            TRUE
          } else {FALSE}
        } else {
          if(nrow(DB$data) < nrow(Database[["Typing"]])) {
            TRUE
          } else {
            FALSE
          }
        }
      } else {FALSE}
    } else {FALSE}
  })
  
  # Render Entry Table Highlights 
  diff_allele <- reactive({
    if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
      var_alleles(select(DB$data, any_of(input$compare_select))) + (13 + nrow(DB$cust_var))
    }
  })
  
  err_thresh <- reactive({
    if (!is.null(DB$data) & !is.null(DB$number_loci)) {
      which(as.numeric(DB$data[["Errors"]]) >= (DB$number_loci * 0.05)) 
    }
  })
  
  err_thresh_na <- reactive({
    if (!is.null(DB$na_table) & !is.null(DB$number_loci)) {
      which(as.numeric(DB$na_table[["Errors"]]) >= (DB$number_loci * 0.05)) 
    }
  })
  
  true_rows <- reactive({
    if (!is.null(DB$data)) {
      which(DB$data$Include == TRUE)
    }
  })
  
  duplicated_names <- reactive({
    if (!is.null(DB$meta)) {
      which(duplicated(DB$meta$`Assembly Name`) | duplicated(DB$meta$`Assembly Name`, fromLast = TRUE))
    }
  })
  
  duplicated_ids <- reactive({
    if (!is.null(DB$meta)) {
      which(duplicated(DB$meta$`Assembly ID`) | duplicated(DB$meta$`Assembly ID`, fromLast = TRUE))
    }
  })
  
  # _______________________ ####
  
  
  ## Startup ----
  
  ### Miscellaneous ----
  
  # Waiting screen config
  waiting_screen <- tagList(
    spin_flower(),
    h4("Loading Database", style = "color: white; cursor: wait")
  )
  
  # Waiter confid
  w <- Waiter$new(
    id = "db_entries",
    html = spin_3(), 
    color = transparent(.5)
  )
  
  #TODO Enable this, or leave disabled
  # Kill server on session end
  session$onSessionEnded( function() {
    stopApp()
  })
  

  ### Logging ----
  # Set log paths
  app_local_share_path <- file.path(path_home(), ".local", "share", "phylotrace")
  logdir <- file.path(app_local_share_path, "logs")
  logfile <- file.path(logdir, "phylotrace.log")
  
  # Initiate logging
  # Create logs dir in user's local share
  if(!dir_exists(logdir)) {
    dir_create(logdir, recurse = TRUE)
  }
  
  # Initiate logging
  logfile <- file.path(file.path(logdir, "phylotrace.log"))
  log <- log_open(logfile, logdir = FALSE)
  log_print("Session started")
  
  
  ### Reactive variables ----
  
  # reactive variables related to startup process
  Startup <- reactiveValues(sidebar = TRUE,
                            block_db = FALSE) 
  
  # reactive variables related to local database
  DB <- reactiveValues()
  
  # reactive variables related to typing process
  Typing <- reactiveValues() 
  
  # Null typing progress trackers
  writeLines("0", file.path(logdir, "script_log.txt"))
  saveRDS(list(), file.path(app_local_share_path, "event_list.rds"))
  
  # reactive variables related to gene screening
  Screening <- reactiveValues()
  
  # reactive variables related to visualization
  Vis <- reactiveValues() 
  
  # reactive variables related to report functions
  Report <- reactiveValues() 
  
  # reactive variables related to scheme functions
  Scheme <- reactiveValues()
  
  ### Set up environment ----
  
  # Get available schemes
  cgmlst_urls <- tryCatch({
    get_latest_url(abb)
  }, error = function(e) {
    DB$failCon <- TRUE
    show_toast(
      title = "Could not retrieve data. Check internet connection.",
      type = "error",
      position = "bottom-end",
      timer = 6000
    )
    warning("Could not retrieve data. Check internet connection.")
    return(NULL)
  })
  
  if(length(cgmlst_urls) > 0) {
    cgmlstorg_schemes$url <- cgmlst_urls
  } else {
    DB$failCon <- TRUE
    show_toast(
      title = "Could not retrieve data. Check internet connection.",
      type = "error",
      position = "bottom-end",
      timer = 6000
    )
    warning("Could not retrieve data. Check internet connection.")
  }
  
  schemes <-  dplyr::arrange(dplyr::add_row(pubmlst_schemes, 
                                            cgmlstorg_schemes), 
                             species)
  
  
  #### Screening environment ----
  
  # Clear screening file
  if(file.exists(file.path(app_local_share_path, "screening", "output_file.tsv"))) {
    file.remove(file.path(app_local_share_path, "screening", "output_file.tsv"))
  }
  
  if(file.exists(file.path(app_local_share_path, "screening", "error.txt"))) {
    file.remove(file.path(app_local_share_path, "screening", "error.txt"))
  }
  
  
  #### Database environment ----
  
  # Load last used database if possible
  if(file.path(app_local_share_path, "last_db.rds") %in% dir_ls(file.path(app_local_share_path))) {
    DB$last_db <- TRUE
  }
  
  observe({
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')  
    
    shinyDirChoose(input,
                   "db_location",
                   roots = c(Home = path_home(), Root = "/"),
                   defaultRoot = "Home",
                   session = session)
    
    if(!is.null(Startup$select_new)) {
      if(isFALSE(Startup$select_new)) {
        if(isFALSE(Startup$block_db)) {
          
          req(input$db_location)
          
          Startup$database <- as.character(
            parseDirPath(
              roots = c(Home = path_home(), Root = "/"),
              input$db_location
            )
          )
          
          # Logical any local database present
          DB$exist <- (length(dir_ls(Startup$database)) == 0)  
          
          # List of local schemes available
          available <- gsub("_", " ", basename(dir_ls(Startup$database)))
          DB$available <- available[available %in% gsub("_", " ", schemes$species)]
        }
        
      } else if(isTRUE(Startup$select_new)) {
        Startup$database <- paste0(DB$new_database, "/Database")
      }
    } else {
      if(!is.null(DB$last_db) & file.exists(file.path(app_local_share_path, "last_db.rds"))) {
        
        last_db <- readRDS(file.path(app_local_share_path, "last_db.rds"))
        
        if(!is.null(last_db) && dir_exists(last_db)) {
          Startup$database <- last_db
          DB$exist <- (length(dir_ls(Startup$database)) == 0)  # Logical any local database present

          # List of local schemes available
          available <- gsub("_", " ", basename(dir_ls(Startup$database)))
          DB$available <- available[available %in% gsub("_", " ", schemes$species)]
        }
      }
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')  
  })
  
  ### Landing page UI ----
  
  # Hide sidebar on startup
  shinyjs::addClass(selector = "body", class = "sidebar-collapse")
  shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
  
  # Show system time
  output$messageMenu <- renderText({
    HTML(format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z"))
  })
  
  observe({
    if (isFALSE(Startup$sidebar)) {
      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
    }
  })
  
  output$start_message <- renderUI(
    column(
      width = 12, 
      align = "center",
      br(), br(), br(), br(), br(), br(),
      div( 
        class = "image",
        imageOutput("imageOutput")
      ),
      br(), br(), br(),
      p(
        HTML(
          paste(
            tags$span(style='color: white; font-size: 16px;', 'Proceed by loading a compatible local database or create a new one.')
          )
        )
      ),
      br(), 
      fluidRow(
        column(
          width = 6,
          align = "right",
          shinyDirButton(
            "db_location",
            "Browse",
            icon = icon("folder-open"),
            title = "Locate the database folder",
            buttonType = "default",
            root = path_home()
          )
        ),
        column(
          width = 6,
          align = "left",
          shinyDirButton(
            "create_new_db",
            "Create New",
            icon = icon("plus"),
            title = "Choose location for new PhyloTrace database",
            buttonType = "default",
            root = path_home()
          )
        )
      ),
      br(), br(),
      fluidRow(
        column(
          width = 12,
          align = "center",
          useWaiter(),
          uiOutput("load_db"),
          br(), br(), br(), br(), br(), br(), br()
        )
      )
    )
  )
  
  # Load db & scheme selection UI
  output$load_db <- renderUI(
    if(!is.null(Startup$select_new)) {
      if(length(DB$new_database) > 0 & Startup$select_new) {
        column(
          width = 12,
          p(
            tags$span(
              style='color: white; font-size: 15px;',
              HTML(
                paste(
                  'New database will be created in',
                  DB$new_database
                )
              )
            )
          ),
          br(),
          actionButton(
            "load",
            "Create",
            class = "load-start"
          )
        )
      } else if(length(DB$available) > 0 & !(Startup$select_new)) {
        if(sum(gsub(" ", "_", gsub(" (PM|CM)", "", DB$available)) %in% gsub("_(PM|CM)", "", schemes$species)) == 0) {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected directory:', Startup$database)
                )
              )
            ),
            br(), 
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Warning: Directory contains no valid elements')
                )
              )
            ),
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Select a database directory containing compatible scheme folders.')
                )
              )
            ),
            br()
          )
        } else if(any(!(gsub(" ", "_", gsub(" (PM|CM)", "", DB$available)) %in% gsub("_(PM|CM)", "", schemes$species)))) {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected:', Startup$database)
                )
              )
            ),
            uiOutput("scheme_db"),
            br(), 
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Warning: Folder contains invalid elements.')
                )
              )
            ),
            br(),
            actionButton(
              "load",
              "Load",
              class = "load-start"
            )
          )
        } else {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected:', Startup$database)
                )
              )
            ),
            uiOutput("scheme_db"),
            br(), br(),
            actionButton(
              "load",
              "Load",
              class = "load-start"
            )
          )
        }
      } else {
        column(
          width = 12,
          p(
            tags$span(
              style='color: white; font-size: 15px; font-style: italic;',
              HTML(
                paste('Selected directory:', Startup$database)
              )
            )
          ),
          br(), 
          p(
            HTML(
              paste(
                tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                          'Warning: Directory contains no valid elements')
              )
            )
          ),
          p(
            HTML(
              paste(
                tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                          'Select a database directory containing compatible scheme folders.')
              )
            )
          ),
          br()
        )
      } 
    } else if((!is.null(DB$last_db)) & (!is.null(DB$available))) {
      if (isTRUE(DB$last_db) & (length(DB$available) > 0)) {
        if(sum(gsub(" ", "_", gsub(" (PM|CM)", "", DB$available)) %in% gsub("_(PM|CM)", "", schemes$species)) == 0) {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected directory:', Startup$database)
                )
              )
            ),
            br(), 
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Warning: Directory contains no valid elements')
                )
              )
            ),
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Select a database containing compatible scheme folders.')
                )
              )
            ),
            br()
          )
        } else if(any(!(gsub(" ", "_", gsub(" (PM|CM)", "", DB$available)) %in% gsub("_(PM|CM)", "", schemes$species)))) {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected directory:', Startup$database)
                )
              )
            ),
            uiOutput("scheme_db"),
            br(), 
            p(
              HTML(
                paste(
                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
                            'Warning: Folder contains invalid elements.')
                )
              )
            ),
            br(),
            actionButton(
              "load",
              "Load",
              class = "load-start"
            )
          )
        } else {
          column(
            width = 12,
            p(
              tags$span(
                style='color: white; font-size: 15px; font-style: italic;',
                HTML(
                  paste('Selected directory:', Startup$database)
                )
              )
            ),
            uiOutput("scheme_db"),
            br(), br(),
            actionButton(
              "load",
              "Load",
              class = "load-start"
            )
          )
        }
      } else if (isTRUE(DB$last_db) & (length(DB$available) == 0)) {
        column(
          width = 12,
          p(
            tags$span(
              style='color: white; font-size: 15px; font-style: italic;',
              HTML(
                paste('Selected directory:', Startup$database)
              )
            )
          ),
          br(),
          actionButton(
            "load",
            "Load",
            class = "load-start"
          )
        )
      }
    }
  )
  
  output$imageOutput <- renderImage({
    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
    list(src = image_path,
         height = 180)
  }, deleteFile = FALSE)
  
  
  ### Landing page events ----
  
  # User selection new db or load db
  observeEvent(input$create_new_db, {
    log_print("Input create_new_db")
    Startup$select_new <- TRUE
  })
  
  observeEvent(input$db_location, {
    log_print("Input db_location")
    Startup$select_new <- FALSE
  })
  
  ### Load app event ----
  
  observeEvent(input$load, {

    if(tail(readLogFile(), 1) != "0") {
      show_toast(
        title = "Pending Multi Typing",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else if(!is.null(Screening$status) && Screening$status == "started") {
      show_toast(
        title = "Pending Gene Screening",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
      output$start_message <- NULL
      output$load_db <- NULL
      
      shinyjs::addClass(selector = "body", class = "sidebar-collapse")
      shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
      
      waiter_show(html = waiting_screen, color = "#384555")
      
      
      #### Reset reactive variables ----
      
      # reactive variables related to local database
      DB$data <- NULL 
      DB$load_selected <- TRUE
      DB$no_na_switch <- FALSE
      DB$first_look <- FALSE
      DB$scheme <- NULL
      DB$check_new_entries <- NULL
      DB$meta_gs <- NULL
      DB$meta <- NULL
      DB$meta_true <- NULL
      DB$allelic_profile <- NULL
      DB$allelic_profile_trunc <- NULL
      DB$allelic_profile_true <- NULL
      DB$scheme_new <- NULL
      DB$loci_info <- NULL
      DB$schemeinfo <- NULL
      DB$scheme_db <- NULL
      DB$scheme_link <- NULL
      DB$number_loci <- NULL
      DB$cluster_thresh <- NULL
      DB$cust_var <- data.frame()
      DB$change <- NULL
      DB$matrix_min <- NULL
      DB$matrix_max <- NULL
      DB$na_table <- NULL
      DB$url_link <- NULL
      if(is.null(DB$failCon)) {DB$failCon <- NULL}
      DB$inhibit_change <- NULL
      DB$count <- NULL
      DB$deleted_entries <- NULL
      DB$remove_iso <- NULL
      DB$ham_matrix <- NULL
      DB$loci <- NULL
      DB$seq <- NULL
      
      # reactive variables related to typing process
      Typing$reload <- NULL
      Typing$multi_sel_table <- NULL
      Typing$pending <- FALSE
      Typing$multi_started <- FALSE
      Typing$multi_help <- FALSE
      Typing$last_success <- "0"
      Typing$last_failure <- "0"
      Typing$last_scheme <- NULL
      Typing$assembly_folder_path <- NULL
      Typing$files_filtered <- NULL
      Typing$assembly_files_path <- NULL
      Typing$result_list <- NULL
      Typing$multi_table_length <- NULL
      Typing$multi_result_status <- NULL
      Typing$last_scheme <- NULL
      Typing$status <- ""
      Typing$file_selection <- ""
      # Null typing progress trackers
      writeLines("0", file.path(logdir, "script_log.txt"))
      saveRDS(list(), file.path(app_local_share_path, "event_list.rds"))
      
      # reactive variables related to gene screening
      Screening$status <- "idle"
      Screening$picker_status <- TRUE
      Screening$first_result <- NULL
      Screening$status_df <- NULL
      Screening$choices <- NULL
      Screening$amr_results <- NULL
      Screening$amr_class <- NULL
      Screening$vir_class <- NULL
      Screening$hm_meta <- NULL
      Screening$res_profile <- NULL
      Screening$picker_choices <- NULL
      Screening$picker_selected <- NULL
      Screening$meta_df <- NULL
      
      # reactive variables related to visualization
      Vis$custom_label_nj <- data.frame()
      Vis$nj_label_pos_y <- list()
      Vis$nj_label_pos_x <- list()
      Vis$nj_label_size <- list()
      Vis$nj <- NULL
      Vis$mst_pre <- NULL
      Vis$title <- NULL
      Vis$nj_max_x <- NULL
      Vis$meta_nj <- NULL
      Vis$nj_parentnodes <- NULL
      Vis$branch_size_nj <- NULL
      Vis$tiplab_padding_nj <- NULL
      Vis$nodepointsize_nj <- NULL
      Vis$tippointsize_nj <- NULL
      Vis$labelsize_nj <- NULL
      Vis$nj_min_x <- NULL
      Vis$amr_nj <- NULL
      Vis$var_cols <- NULL
      Vis$meta_mst <- NULL
      Vis$unique_meta <- NULL
      Vis$nj_heatmap_select <- NULL
      Vis$nj_plot <- NULL
      Vis$nj_tree <- NULL
      
      # Reactive variables related to plot controls
      if(isTRUE(Vis$mst_true)) {
        mst_node_label_reactive("Assembly Name")
        mst_title_reactive("")
        mst_subtitle_reactive("")
        mst_color_var_reactive(FALSE)
        mst_col_var_reactive("Isolation Date")
        mst_col_scale_reactive("Viridis")
        mst_text_color_reactive("#000000")
        mst_color_node_reactive("#B2FACA")
        mst_color_edge_reactive("#000000")
        mst_edge_font_color_reactive("#000000")
        mst_background_color_reactive("#ffffff")
        mst_background_transparent_reactive(FALSE)
        mst_scale_nodes_reactive(TRUE)
        mst_node_scale_reactive(c(20, 40))
        mst_node_size_reactive(30)
        mst_scale_edges_reactive(TRUE)
        mst_edge_length_scale_reactive(15)
        mst_edge_length_reactive(35)
        mst_edge_font_size_reactive(18)
        mst_node_label_fontsize_reactive(14)
        mst_title_size_reactive(35)
        mst_subtitle_size_reactive(20)
        mst_ratio_reactive(16/10)
        mst_scale_reactive(600)
        mst_shadow_reactive(TRUE)
        mst_node_shape_reactive("dot")
        mst_show_clusters_reactive(FALSE)
        mst_cluster_col_scale_reactive("Viridis")
        mst_cluster_type_reactive("Area")
        mst_cluster_width_reactive(24)
        ifelse(!is.null(DB$cluster_thresh),
               mst_cluster_threshold_reactive(DB$cluster_thresh),
               mst_cluster_threshold_reactive(10))
        mst_legend_ori_reactive("left")
        mst_font_size_reactive(18)
        mst_symbol_size_reactive(20)
      }
      
      if(isTRUE(Vis$nj_true)) {
        # Tip label
        Vis$nj_tiplab_val_reset <- TRUE
        nj_tiplab_val("Assembly Name")
        nj_tiplab_show_val(TRUE)
        Vis$nj_align_reset <- TRUE
        nj_align_val(FALSE)
        ifelse(!is.null(Vis$labelsize_nj),
               nj_tiplab_size_val(Vis$labelsize_nj),
               nj_tiplab_size_val(4))
        nj_tiplab_fontface_val("plain")
        nj_tiplab_alpha_val(1)
        nj_tiplab_position_val(0)
        Vis$nj_tiplab_angle_reset <- TRUE
        nj_tiplab_angle_val(0)
        
        # Label panels
        nj_geom_val(FALSE)
        nj_tiplab_labelradius_val(0.2)
        ifelse(!is.null(Vis$tiplab_padding_nj),
               nj_tiplab_padding_val(Vis$tiplab_padding_nj),
               nj_tiplab_padding_val(0.2))
        
        # Branch labels
        nj_show_branch_label_val(FALSE)
        ifelse(!is.null(Vis$branch_size_nj),
               nj_branch_size_val(Vis$branch_size_nj),
               nj_branch_size_val(4))
        Vis$nj_branch_label_val_reset <- TRUE
        nj_branch_label_val("Host")
        nj_branchlab_alpha_val(0.65)
        nj_branch_x_val(0)
        nj_branchlab_fontface_val("plain")
        nj_branch_labelradius_val(0.5)
        
        # Titles
        nj_title_val(NULL)
        nj_title_size_val(30)
        nj_subtitle_val(NULL)
        nj_subtitle_size_val(30)
        
        # Custom label
        Vis$nj_label_pos_x <- list()
        Vis$nj_label_pos_y <- list()
        Vis$nj_label_size <- list()
        Vis$custom_label_nj <- data.frame()
        
        # Tip label mapping
        nj_mapping_show_val(FALSE)
        Vis$nj_color_mapping_val_reset <- TRUE
        nj_color_mapping_val("Country")
        Vis$nj_tiplab_scale_reset <- TRUE
        nj_tiplab_scale_val(nj_tiplab_scale_val_default())
        Vis$nj_color_mapping_div_mid_reset <- TRUE
        nj_color_mapping_div_mid_val("Mean")
        
        # Tip points mapping
        nj_tipcolor_mapping_show_val(FALSE)
        Vis$nj_tipcolor_mapping_val_reset <- TRUE
        nj_tipcolor_mapping_val("Country")
        Vis$nj_tippoint_scale_val_reset <- TRUE
        nj_tippoint_scale_val(nj_tippoint_scale_val_default())
        Vis$nj_tipcolor_mapping_div_mid_reset <- TRUE
        nj_tipcolor_mapping_div_mid_val("Mean")
        
        # Tip shape mapping
        nj_tipshape_mapping_show_val(FALSE)
        Vis$nj_tipshape_mapping_val_reset <- TRUE
        nj_tipshape_mapping_val("Host")
        
        # Tiles mapping
        nj_tiles_show_1_val(FALSE)
        nj_tiles_show_2_val(FALSE)
        nj_tiles_show_3_val(FALSE)
        nj_tiles_show_4_val(FALSE)
        nj_tiles_show_5_val(FALSE)
        Vis$nj_fruit_variable_val_reset <- TRUE
        nj_fruit_variable_val("Isolation Date")
        Vis$nj_fruit_variable_2_val_reset <- TRUE
        nj_fruit_variable_2_val("Isolation Date")
        Vis$nj_fruit_variable_3_val_reset <- TRUE
        nj_fruit_variable_3_val("Isolation Date")
        Vis$nj_fruit_variable_4_val_reset <- TRUE
        nj_fruit_variable_4_val("Isolation Date")
        Vis$nj_fruit_variable_5_val_reset <- TRUE
        nj_fruit_variable_5_val("Isolation Date")
        Vis$nj_tiles_scale_1_reset <- TRUE
        nj_tiles_scale_1_val(nj_tiles_scale_1_val_default())
        Vis$nj_tiles_scale_2_reset <- TRUE
        nj_tiles_scale_2_val(nj_tiles_scale_2_val_default())
        Vis$nj_tiles_scale_3_reset <- TRUE
        nj_tiles_scale_3_val(nj_tiles_scale_3_val_default())
        Vis$nj_tiles_scale_4_reset <- TRUE
        nj_tiles_scale_4_val(nj_tiles_scale_4_val_default())
        Vis$nj_tiles_scale_5_reset <- TRUE
        nj_tiles_scale_5_val(nj_tiles_scale_5_val_default())
        Vis$nj_tiles_mapping_div_mid_1_reset <- TRUE
        nj_tiles_mapping_div_mid_1_val("Mean")
        Vis$nj_tiles_mapping_div_mid_2_reset <- TRUE
        nj_tiles_mapping_div_mid_2_val("Mean")
        Vis$nj_tiles_mapping_div_mid_3_reset <- TRUE
        nj_tiles_mapping_div_mid_3_val("Mean")
        Vis$nj_tiles_mapping_div_mid_4_reset <- TRUE
        nj_tiles_mapping_div_mid_4_val("Mean")
        Vis$nj_tiles_mapping_div_mid_5_reset <- TRUE
        nj_tiles_mapping_div_mid_5_val("Mean")
        
        nj_heatmap_show_val(FALSE)
        Vis$nj_heatmap_select_val_reset <- TRUE
        nj_heatmap_select_val(NULL)
        Vis$nj_heatmap_scale_reset <- TRUE
        nj_heatmap_scale_val(nj_heatmap_scale_val_default())
        Vis$nj_heatmap_div_mid_val_reset <- TRUE
        nj_heatmap_div_mid_val("Mean")
        
        # Color values
        nj_color_val("#000000")
        nj_bg_val("#ffffff")
        nj_title_color_val("#000000")
        nj_tiplab_color_val("#000000")
        nj_tiplab_fill_val("#84D9A0")
        nj_branch_label_color_val("#FFB7B7")
        nj_tippoint_color_val("#3A4657")
        nj_nodepoint_color_val("#3A4657")
        
        # Tip points
        nj_tippoint_show_val(FALSE)
        Vis$nj_tippoint_shape_reset <- TRUE
        nj_tippoint_shape_val("circle")
        nj_tippoint_alpha_val(0.5)
        ifelse(!is.null(Vis$tippointsize_nj),
               nj_tippoint_size_val(Vis$tippointsize_nj),
               nj_tippoint_size_val(4))
        
        # Node points
        nj_nodepoint_show_val(FALSE)
        nj_nodepoint_shape_val("circle")
        nj_nodepoint_alpha_val(1)
        ifelse(!is.null(Vis$nodepointsize_nj),
               nj_nodepoint_size_val(Vis$nodepointsize_nj),
               nj_nodepoint_size_val(2.5))
        
        # Tiles
        nj_tile_number_val(1)
        nj_fruit_alpha_val(1)
        nj_fruit_alpha_2_val(1)
        nj_fruit_alpha_3_val(1)
        nj_fruit_alpha_4_val(1)
        nj_fruit_alpha_5_val(1)
        Vis$nj_fruit_width_circ_val_reset <- TRUE
        nj_fruit_width_circ_val(fruit_width())
        Vis$nj_fruit_width_circ_2_val_reset <- TRUE
        nj_fruit_width_circ_2_val(fruit_width())
        Vis$nj_fruit_width_circ_3_val_reset <- TRUE
        nj_fruit_width_circ_3_val(fruit_width())
        Vis$nj_fruit_width_circ_4_val_reset <- TRUE
        nj_fruit_width_circ_4_val(fruit_width())
        Vis$nj_fruit_width_circ_5_val_reset <- TRUE
        nj_fruit_width_circ_5_val(fruit_width())
        Vis$nj_fruit_offset_circ_reset <- TRUE
        nj_fruit_offset_circ_val(0.05)
        Vis$nj_fruit_offset_circ_2_reset <- TRUE
        nj_fruit_offset_circ_2_val(0.05)
        Vis$nj_fruit_offset_circ_3_reset <- TRUE
        nj_fruit_offset_circ_3_val(0.05)
        Vis$nj_fruit_offset_circ_4_reset <- TRUE
        nj_fruit_offset_circ_4_val(0.05)
        Vis$nj_fruit_offset_circ_5_reset <- TRUE
        nj_fruit_offset_circ_5_val(0.05)
        
        # Heatmap
        nj_heatmap_title_val("Heatmap")
        nj_colnames_angle_val(-90)
        Vis$nj_colnames_y_val_reset <- TRUE
        nj_colnames_y_val(-1)
        nj_heatmap_width_val(heatmap_width())
        Vis$nj_heatmap_offset_val_reset <- TRUE
        nj_heatmap_offset_val(0)
        
        # Clade highlights
        nj_nodelabel_show_val(FALSE)
        Vis$nj_parentnode_val_reset <- TRUE
        nj_parentnode_val("")
        nj_clade_scale_val(clade_highlight_color())
        nj_clade_type_val("roundrect")
        
        # Dimensions
        nj_ratio_val(c("16:10" = (16 / 10)))
        nj_v_val(0)
        nj_h_val(-0.05)
        nj_scale_val(670)
        nj_zoom_val(0.95)
        nj_layout_val("rectangular")
        nj_rootedge_show_val(FALSE)
        Vis$nj_rootedge_length_val_reset <- TRUE
        ifelse(!is.null(Vis$nj_max_x),
               nj_rootedge_length_val(round(ceiling(Vis$nj_max_x) * 0.05)),
               nj_rootedge_length_val(2))
        nj_rootedge_line_val("solid")
        Vis$nj_xlim_val_reset <- TRUE
        nj_xlim_val(-10)
        Vis$nj_xlim_inw_val_reset <- TRUE
        nj_xlim_inw_val(50)
        nj_treescale_show_val(FALSE)
        Vis$nj_treescale_width_val_reset <- TRUE
        ifelse(!is.null(Vis$nj_max_x),
               nj_treescale_width_val(round(ceiling(Vis$nj_max_x) * 0.1, 0)),
               nj_treescale_width_val(2))
        Vis$nj_treescale_x_val_reset <- TRUE
        ifelse(!is.null(Vis$nj_max_x),
               nj_treescale_x_val(round(ceiling(Vis$nj_max_x) * 0.2, 0)),
               nj_treescale_x_val(2))
        Vis$nj_treescale_y_val_reset <- TRUE
        nj_treescale_y_val(0)
        nj_ladder_val(TRUE)
        
        # Legend
        nj_legend_orientation_val("vertical")
        nj_legend_size_val(10)
        nj_legend_x_val(0.9)
        nj_legend_y_val(0.2)
      }
      
      # reactive variables related to report functions
      Report$report_list_mst <- NULL
      Report$report_list_nj <- NULL
      Report$report_df <- NULL
      
      # reactive variables related to scheme functions
      Scheme$link_scheme <- NULL
      Scheme$link_cgmlst <- NULL
      Scheme$link_targets <- NULL
      Scheme$folder_name <- NULL
      Scheme$species_data <- NULL
      
      
      ### Reset UI elements ----
      
      # Reset reactive screening variables 
      output$screening_start <- NULL
      output$screening_result_sel <- NULL
      output$screening_result <- NULL
      output$screening_fail <- NULL
      output$multi_select_table <- NULL
      output$multi_select_tab_ctrls <- NULL
      Screening$status_df <- NULL
      Screening$choices <- NULL
      Screening$picker_status <- TRUE
      Screening$status <- "idle"
      Screening$first_result <- NULL
      if(!is.null(input$screening_select)) {
        if(!is.null(DB$data)) {
          updatePickerInput(session, "screening_select", selected = character(0))
        }
      }
      
      # Empty tree plot fields
      output$tree_field <- NULL
      output$mst_field <- NULL
      log_print("Input load")
      
      # set typing start control variable
      Typing$reload <- TRUE
      
      
      ### Render status bar ----
      observe({
        req(DB$scheme)
        
        if(is.null(input$scheme_position)) {
          output$loaded_scheme <- renderUI({
            fluidRow(
              tags$li(
                class = "dropdown", 
                tags$span(HTML(
                  paste('<i class="fa-solid fa-layer-group"></i>', 
                        "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
                        DB$scheme,
                        "</i>")), 
                  style = "color:black;")
              )
            )
          })
        } 
        
        if(!is.null(input$scheme_position)) {
          output$loaded_scheme <- renderUI({
            fluidRow(
              tags$li(
                class = "dropdown", 
                tags$span(HTML(
                  paste('<i class="fa-solid fa-layer-group"></i>', 
                        "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
                        DB$scheme,
                        "</i>")), 
                  style = "color:black;"),
                div(
                  class = "reload-bttn",
                  style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
                  tipify(
                    actionButton(
                      "reload_db",
                      label = "",
                      icon = icon("rotate")
                    ),
                    title = "Change scheme",
                    options = list("delay': 400, 'foo" = "foo")
                  )
                )
              )
            )
          })
        }
      })
      
      observe({
        if(!is.null(Startup$database) && length(Startup$database) > 0){
          if(nchar(Startup$database) > 35) {
            database <- paste0(substring(Startup$database, first = 1, last = 35), "...")
          } else {
            database <- Startup$database
          }
          output$databasetext <- renderUI({
            fluidRow(
              tags$li(
                class = "dropdown", 
                tags$span(HTML(
                  paste('<i class="fa-solid fa-folder-open"></i>', 
                        "Database:&nbsp;&nbsp;&nbsp;<i>",
                        database,
                        "</i>")), 
                  style = "color:black;")
              ),
              if(nchar(database) > 35) {bsTooltip("databasetext", 
                                                  HTML(Startup$database), 
                                                  placement = "bottom", 
                                                  trigger = "hover")}
            )
          })
        }
      })
      
      observe({
        if(!is.null(Startup$database)) {
          if(Typing$status == "Finalized"){
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
                    style = "color:black;")
                )
              )
            )
          } else if(Typing$status == "Attaching"){
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
                    style = "color:black;")
                )
              )
            )
          } else if(Typing$status == "Processing") {
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
                    style = "color:black;")
                )
              )
            )
          } else if(Screening$status == "started") {
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
                    style = "color:black;")
                )
              )
            )
          } else if(Screening$status == "finished") {
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
                    style = "color:black;")
                )
              )
            )
          } else {
            output$statustext <- renderUI(
              fluidRow(
                tags$li(
                  class = "dropdown", 
                  tags$span(HTML(
                    paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
                          "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
                    style = "color:black;")
                )
              )
            )
          }    
        }
      })
      
      shinyjs::runjs(
        'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
            // Select the span element
            let spanElement = document.querySelector("#loaded_scheme > div > li > span");
                      
            // Get the bounding rectangle of the span element
            let rect = spanElement.getBoundingClientRect();
            
            // Extract the width
            let width = rect.width;
            
            Shiny.setInputValue("scheme_position", width);            
          }'
      )
      
      # Load app elements based on database availability and missing value presence
      if(isTRUE(Startup$select_new) && !is.null(DB$new_database)) {
        if(file.path(DB$new_database, "Database") %in% dir_ls(DB$new_database)) {
          log_print("Directory already contains a database")
          
          show_toast(
            title = "Directory already contains a database",
            type = "error",
            position = "bottom-end",
            timer = 6000
          )
          DB$load_selected <- FALSE
        } else {
          if(Startup$select_new | (isFALSE(Startup$select_new) & is.null(input$scheme_db))) {
            
            log_print(paste0("New database created in ", DB$new_database))
            
            DB$check_new_entries <- TRUE
            DB$data <- NULL
            DB$meta_gs <- NULL
            DB$meta <- NULL
            DB$meta_true <- NULL
            DB$allelic_profile <- NULL
            DB$allelic_profile_trunc <- NULL
            DB$allelic_profile_true <- NULL
            
            # null Distance matrix, entry table and plots
            output$db_distancematrix <- NULL 
            output$db_entries_table <- NULL
            output$tree_mst <- NULL
            output$tree_plot <- NULL
            
            # null report values
            Report$report_list_mst <- list()
            Report$report_list_nj <- list()
            
            # null plots
            Vis$nj <- NULL
            Vis$mst_pre <- NULL
            
            removeModal()
            
            ### Render Menu Items ----
            
            Startup$sidebar <- FALSE
            
            output$menu_header_typing <- NULL
            output$menu_header_screening <- NULL
            
            # Hide start message
            output$start_message <- NULL
            
            DB$load_selected <- FALSE
            
            # Declare database path
            Startup$database <- file.path(DB$new_database, "Database")
            
            # Set database availability screening variables to present database
            Startup$block_db <- TRUE
            Startup$select_new <- FALSE
            
            # Render menu with Manage Schemes as start tab and no Missing values tab
            output$menu_typing <- renderMenu(
              sidebarMenu(
                menuItem(
                  text = "Schemes",
                  tabName = "init",
                  icon = icon("layer-group"),
                  selected = TRUE
                )
              )
            )
            
            # Show message that loci files are missing
            showModal(
              div(
                class = "start-modal",
                modalDialog(
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px; display: block;">',
                            "Download a cgMLST scheme to add a new folder in the database directory.",
                            " Multiple schemes can be downloaded and included in one database.",
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  ),
                  title = paste("Set Up New Database"),
                  fade = TRUE,
                  easyClose = TRUE,
                  footer = tagList(
                    modalButton("Okay")
                  )
                )
              )
            )
            
            # Dont render these elements
            output$db_no_entries <- NULL
            output$distancematrix_no_entries <- NULL
            output$db_entries <- NULL
            output$edit_index <- NULL
            output$edit_scheme_d <- NULL
            output$edit_entries <- NULL
            output$compare_select <- NULL
            output$delete_select <- NULL
            output$del_bttn <- NULL
            output$compare_allele_box <- NULL
            output$download_entries <- NULL
            output$missing_values <- NULL
            output$custom_var_box <- NULL
            output$delete_box <- NULL
            output$missing_values_sidebar <- NULL
            output$download_scheme_info <- NULL
            output$download_loci <- NULL
            output$entry_table_controls <- NULL
            output$multi_stop <- NULL
            output$metadata_multi_box <- NULL
            output$start_multi_typing_ui <- NULL
            output$pending_typing <- NULL
            output$multi_typing_results <- NULL
            output$single_typing_progress <- NULL
            output$metadata_single_box <- NULL
            output$start_typing_ui <- NULL
          }
        }
      } else {
        log_print(paste0("Loading existing ", input$scheme_db, " database from ", Startup$database))
      }
      
      if(isTRUE(DB$load_selected)) {
        #Check if selected scheme valid
        if(gsub(" ", "_", gsub(" (PM|CM)", "", input$scheme_db)) %in% gsub("_(PM|CM)", "", schemes$species)) {
          
          # Save database path for next start
          saveRDS(Startup$database, file.path(app_local_share_path, "last_db.rds"))
          
          DB$check_new_entries <- TRUE
          DB$data <- NULL
          DB$meta_gs <- NULL
          DB$meta <- NULL
          DB$meta_true <- NULL
          DB$allelic_profile <- NULL
          DB$allelic_profile_trunc <- NULL
          DB$allelic_profile_true <- NULL
          
          if(!identical(DB$scheme, input$scheme_db)) {
            DB$scheme <- input$scheme_db
            DB$scheme_new <- TRUE
          }
          
          # Load AMR profile
          profile_path <- file.path(Startup$database, gsub(" ", "_", DB$scheme), "AMR_Profile.rds")
          if(file.exists(profile_path)) {
            amr_profile <- readRDS(profile_path)
            Screening$amr_results <- amr_profile$results
            Screening$amr_class <- amr_profile$AMR_classification
            Screening$vir_class <- amr_profile$virulence_classification
          }
          
          # null Distance matrix, entry table and plots
          output$db_distancematrix <- NULL 
          output$db_entries_table <- NULL
          output$tree_mst <- NULL
          output$tree_plot <- NULL
          
          # null typing initiation UI
          output$multi_stop <- NULL
          output$metadata_multi_box <- NULL
          output$start_multi_typing_ui <- NULL
          output$pending_typing <- NULL
          output$multi_typing_results <- NULL
          output$single_typing_progress <- NULL
          output$metadata_single_box <- NULL
          output$start_typing_ui <- NULL
          
          # null report values
          Report$report_list_mst <- list()
          Report$report_list_nj <- list()
          
          # null plots
          Vis$nj <- NULL
          Vis$mst_pre <- NULL
          
          removeModal()
          
          Startup$sidebar <- FALSE
          
          output$menu_header_typing <- renderUI(
            div(
              class = "menu-header-typing",
              HTML(
                paste(
                  tags$span(style="color: white; font-size: 14px; position: relative; top: 8px; margin-left: 10px;", "cgMLST Typing")
                )
              )
            )
          )
          
          output$menu_header_screening <- renderUI(
            div(
              class = "menu-header-screening",
              HTML(
                paste(
                  tags$span(style="color: white; font-size: 14px; position: relative; top: 8px; margin-left: 10px;", "Locus Screening")
                )
              )
            )
          )
          
          # Hide start message
          output$start_message <- NULL
          
          if(any(grepl(gsub(" ", "_", DB$scheme), dir_ls(Startup$database)))) {
            
            if(!any(grepl("alleles", dir_ls(paste0(
              Startup$database, "/", 
              gsub(" ", "_", DB$scheme)))))) {
              
              log_print("Missing loci files")
              
              # Show message that loci files are missing
              showModal(
                div(
                  class = "start-modal",
                  modalDialog(
                    fluidRow(
                      br(), 
                      column(
                        width = 11,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px; margin-left: 15px; display: block;">',
                              "No loci files are present in the local ", 
                              DB$scheme, 
                              " folder. Download the scheme again (no influence on already typed assemblies).",
                              '</span>'
                            )
                          )
                        )
                      ),
                      br()
                    ),
                    title = "Local Database Error",
                    fade = TRUE,
                    easyClose = TRUE,
                    footer = tagList(
                      modalButton("Okay")
                    )
                  )
                )
              )
              
              # Render menu with Manage Schemes as start tab
              output$menu_typing <- renderMenu(
                sidebarMenu(
                  menuItem(
                    text = "Database",
                    tabName = "database",
                    icon = icon("hard-drive"),
                    startExpanded = TRUE,
                    menuSubItem(
                      text = "Browse Entries",
                      tabName = "db_browse_entries"
                    ),
                    menuSubItem(
                      text = "Scheme Info",
                      tabName = "db_schemeinfo"
                    ),
                    menuSubItem(
                      text = "Loci Info",
                      tabName = "db_loci_info"
                    ),
                    menuSubItem(
                      text = "Distance Matrix",
                      tabName = "db_distmatrix"
                    ),
                    if(!is.null(DB$allelic_profile)) {
                      if(anyNA(DB$allelic_profile)) {
                        menuSubItem(
                          text = "Missing Values",
                          tabName = "db_missing_values",
                          icon = icon("triangle-exclamation")
                        )
                      }
                    }
                  ),
                  menuItem(
                    text = "Schemes",
                    tabName = "init",
                    icon = icon("layer-group"),
                    selected = TRUE
                  ),
                  menuItem(
                    text = "Allelic Typing",
                    tabName = "typing",
                    icon = icon("gears")
                  ),
                  menuItem(
                    text = "Visualization",
                    tabName = "visualization",
                    icon = icon("circle-nodes")
                  )
                )
              )
              
              if(!is.null(DB$scheme)) {
                amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                 amrfinder_species = amrfinder_species)
                
                if(!isFALSE(amrfinder_available)) {
                  
                  output$menu_screening <- renderMenu(screening_menu_available)
                  
                } else {
                  output$menu_screening <- renderMenu(screening_menu_available)
                }
              }
            } else if (!file.exists(file.path(Startup$database, 
                                              gsub(" ", "_", DB$scheme),
                                              "scheme_info.rds"))) {
              
              output$download_scheme_info <- NULL
              
              log_print("Scheme info file missing")
              
              # Show message that scheme info is missing
              showModal(
                div(
                  class = "start-modal",
                  modalDialog(
                    fluidRow(
                      br(), 
                      column(
                        width = 11,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px; display: block; margin-left: 15px;">',
                              "Scheme info of the local ", 
                              DB$scheme, 
                              " database is missing. Download the scheme again (no influence on already typed assemblies).",
                              '</span>'
                            )
                          )
                        )
                      ),
                      br()
                    ),
                    title = "Local Database Error",
                    fade = TRUE,
                    easyClose = TRUE,
                    footer = tagList(
                      modalButton("Okay")
                    )
                  )
                )
              )
              
              # Render menu with Manage Schemes as start tab
              output$menu_typing <- renderMenu(
                sidebarMenu(
                  menuItem(
                    text = "Database",
                    tabName = "database",
                    icon = icon("hard-drive"),
                    startExpanded = TRUE,
                    menuSubItem(
                      text = "Browse Entries",
                      tabName = "db_browse_entries"
                    ),
                    menuSubItem(
                      text = "Scheme Info",
                      tabName = "db_schemeinfo"
                    ),
                    menuSubItem(
                      text = "Loci Info",
                      tabName = "db_loci_info"
                    ),
                    menuSubItem(
                      text = "Distance Matrix",
                      tabName = "db_distmatrix"
                    ),
                    if(!is.null(DB$allelic_profile)) {
                      if(anyNA(DB$allelic_profile)) {
                        menuSubItem(
                          text = "Missing Values",
                          tabName = "db_missing_values",
                          icon = icon("triangle-exclamation")
                        )
                      }
                    }
                  ),
                  menuItem(
                    text = "Schemes",
                    tabName = "init",
                    icon = icon("layer-group"),
                    selected = TRUE
                  ),
                  menuItem(
                    text = "Allelic Typing",
                    tabName = "typing",
                    icon = icon("gears")
                  ),
                  menuItem(
                    text = "Visualization",
                    tabName = "visualization",
                    icon = icon("circle-nodes")
                  )
                )
              )
              
              if(!is.null(DB$scheme)) {
                amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                 amrfinder_species = amrfinder_species)
                
                if(!isFALSE(amrfinder_available)) {
                  
                  output$menu_screening <- renderMenu(screening_menu_available)
                  
                } else {
                  output$menu_screening <- renderMenu(screening_menu_available)
                }
              }
              
            } else {
              
              # Produce Loci Info Table
              if(file.exists(file.path(Startup$database, 
                                       gsub(" ", "_", DB$scheme), 
                                       "targets.csv"))) {
                DB$loci_info <- read.csv(
                  file.path(Startup$database, gsub(" ", "_", DB$scheme), "targets.csv"),
                  header = TRUE,
                  sep = "\t",
                  row.names = NULL,
                  colClasses = c(
                    "NULL",
                    "character",
                    "character",
                    "integer",
                    "integer",
                    "character",
                    "integer",
                    "NULL"
                  )
                ) 
              } else {
                DB$loci_info <- NULL
              }
              
              # Produce Scheme Info Table
              if(file.exists(file.path(Startup$database, 
                                       gsub(" ", "_", DB$scheme),
                                       "scheme_info.rds"))) {
                
                DB$schemeinfo <- readRDS(file.path(Startup$database, 
                                                   gsub(" ", "_", DB$scheme), 
                                                   "scheme_info.rds"))
                
                # Get scheme database link
                DB$scheme_db <- DB$schemeinfo[,2][DB$schemeinfo[,1] == "Database"]
                
                # Get scheme database link
                DB$scheme_link <- str_extract(DB$schemeinfo[,2][DB$schemeinfo[,1] == "URL"], 
                                              '(?<=href=")[^"]+')
                
                # Get locus count
                number_loci <- DB$schemeinfo[, 2][DB$schemeinfo[,1] == "Locus Count"]
                
                if(DB$scheme_db == "cgMLST.org Nomenclature Server (h25)") {
                  # Locus count
                  DB$number_loci <- as.numeric(gsub(",", "", number_loci))
                  
                  # Cluster threshold
                  DB$cluster_thresh <- DB$schemeinfo[,2][DB$schemeinfo[,1] == "Complex Type Distance"]
                  
                } else if(DB$scheme_db == "pubMLST") {
                  # Locus count
                  DB$number_loci <- as.numeric(number_loci)
                  
                  # Cluster threshold
                  DB$cluster_thresh <- 10
                }
                
              } else {
                log_print(paste0("Scheme info file missing in the local ", DB$scheme, " folder"))
                
                # Show message that loci files are missing
                showModal(
                  div(
                    class = "start-modal",
                    modalDialog(
                      fluidRow(
                        br(), 
                        column(
                          width = 11,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                                "Scheme info file is missing in the local ", 
                                DB$scheme, 
                                " folder. Download the scheme again (no influence on already typed assemblies).",
                                '</span>'
                              )
                            )
                          )
                        ),
                        br()
                      ),
                      title = "Local Database Error",
                      fade = TRUE,
                      easyClose = TRUE,
                      footer = tagList(
                        modalButton("Okay")
                      )
                    )
                  )
                )
              } 
              
              # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
              if(DB$number_loci > length(dir_ls(paste0(Startup$database, 
                                                       "/", 
                                                       gsub(" ", "_", DB$scheme), 
                                                       "/", 
                                                       gsub(" ", "_", DB$scheme), 
                                                       "_alleles")))) {
                
                log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
                
                # Show message that loci files are missing
                showModal(
                  div(
                    class = "start-modal",
                    modalDialog(
                      fluidRow(
                        br(), 
                        column(
                          width = 11,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                                "Some loci files are missing in the local ", 
                                DB$scheme, 
                                " folder. Download the scheme again (no influence on already typed assemblies).",
                                '</span>'
                              )
                            )
                          )
                        ),
                        br()
                      ),
                      title = "Local Database Error",
                      fade = TRUE,
                      easyClose = TRUE,
                      footer = tagList(
                        modalButton("Okay")
                      )
                    )
                  )
                )
                
                # Render menu with Manage Schemes as start tab
                output$menu_typing <- renderMenu(
                  sidebarMenu(
                    menuItem(
                      text = "Database",
                      tabName = "database",
                      icon = icon("hard-drive"),
                      startExpanded = TRUE,
                      menuSubItem(
                        text = "Browse Entries",
                        tabName = "db_browse_entries"
                      ),
                      menuSubItem(
                        text = "Scheme Info",
                        tabName = "db_schemeinfo"
                      ),
                      menuSubItem(
                        text = "Loci Info",
                        tabName = "db_loci_info"
                      ),
                      menuSubItem(
                        text = "Distance Matrix",
                        tabName = "db_distmatrix"
                      ),
                      if(!is.null(DB$allelic_profile)) {
                        if(anyNA(DB$allelic_profile)) {
                          menuSubItem(
                            text = "Missing Values",
                            tabName = "db_missing_values",
                            icon = icon("triangle-exclamation")
                          )
                        }
                      }
                    ),
                    menuItem(
                      text = "Schemes",
                      tabName = "init",
                      icon = icon("layer-group"),
                      selected = TRUE
                    ),
                    menuItem(
                      text = "Allelic Typing",
                      tabName = "typing",
                      icon = icon("gears")
                    ),
                    menuItem(
                      text = "Visualization",
                      tabName = "visualization",
                      icon = icon("circle-nodes")
                    )
                  )
                )
                
                if(!is.null(DB$scheme)) {
                  amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                   amrfinder_species = amrfinder_species)
                  
                  if(!isFALSE(amrfinder_available)) {
                    
                    output$menu_screening <- renderMenu(screening_menu_available)
                    
                  } else {
                    output$menu_screening <- renderMenu(screening_menu_available)
                  }
                }
                
              } else {
                
                ###### All checks passed - load database
                # If typed entries present
                if (any(grepl("Typing.rds", 
                              dir_ls(paste0(Startup$database, "/", 
                                            gsub(" ", "_", DB$scheme)))))) {
                  
                  # Load database from files  
                  Database <- readRDS(file.path(Startup$database, 
                                                gsub(" ", "_", DB$scheme), 
                                                "Typing.rds"))
                  
                  DB$data <- Database[["Typing"]]
                  
                  if(!is.null(DB$data)){
                    if ((ncol(DB$data)-13) != DB$number_loci) {
                      cust_var <- select(DB$data, 14:(ncol(DB$data) - DB$number_loci))
                      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
                    } else {
                      DB$cust_var <- data.frame()
                    }
                  }
                  
                  DB$change <- FALSE
                  DB$meta_gs <- select(DB$data, c(1, 3:13))
                  DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
                  DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
                  DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
                  DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
                  DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
                  
                  # Reset other reactive typing variables
                  output$single_typing_progress <- NULL
                  output$typing_fin <- NULL
                  output$single_typing_results <- NULL
                  output$typing_formatting <- NULL
                  
                  # Check need for new missing value display
                  if(isTRUE(Startup$first_look)) {
                    if(sum(apply(DB$data, 1, anyNA)) >= 1) {
                      DB$no_na_switch <- TRUE
                    } else {
                      DB$no_na_switch <- FALSE
                    }
                  }
                  
                  Startup$first_look <- TRUE
                  
                  output$initiate_typing_ui <- renderUI({
                    column(
                      width = 3,
                      align = "center",
                      br(),
                      br(),
                      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
                      br(),
                      br(),
                      p(
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
                          )
                        )
                      ),
                      fluidRow(
                        column(1),
                        column(
                          width = 11,
                          align = "center",
                          shinyFilesButton(
                            "genome_file",
                            "Browse" ,
                            icon = icon("file"),
                            title = "Select the assembly in .fasta/.fna/.fa format:",
                            multiple = FALSE,
                            buttonType = "default",
                            class = NULL,
                            root = path_home()
                          ),
                          br(),
                          br(),
                          uiOutput("genome_path"),
                          br()
                        )
                      )
                    )
                  })
                  
                  output$initiate_multi_typing_ui <- initiate_multi_typing_ui
                  
                  if(!anyNA(DB$allelic_profile)) {
                    
                    # no NA's -> dont render missing values sidebar elements
                    output$missing_values_sidebar <- NULL
                    
                    # Render menu if no NA's present
                    output$menu_typing <- renderMenu(
                      sidebarMenu(
                        menuItem(
                          text = "Database",
                          tabName = "database",
                          icon = icon("hard-drive"),
                          startExpanded = TRUE,
                          menuSubItem(
                            text = "Browse Entries",
                            tabName = "db_browse_entries"
                          ),
                          menuSubItem(
                            text = "Scheme Info",
                            tabName = "db_schemeinfo"
                          ),
                          menuSubItem(
                            text = "Loci Info",
                            tabName = "db_loci_info"
                          ),
                          menuSubItem(
                            text = "Distance Matrix",
                            tabName = "db_distmatrix"
                          )
                        ),
                        menuItem(
                          text = "Schemes",
                          tabName = "init",
                          icon = icon("layer-group")
                        ),
                        menuItem(
                          text = "Allelic Typing",
                          tabName = "typing",
                          icon = icon("gears")
                        ),
                        menuItem(
                          text = "Visualization",
                          tabName = "visualization",
                          icon = icon("circle-nodes")
                        )
                      )
                    )
                    
                    if(!is.null(DB$scheme)) {
                      amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                       amrfinder_species = amrfinder_species)
                      
                      if(!isFALSE(amrfinder_available)) {
                        
                        output$menu_screening <- renderMenu(screening_menu_available)
                        
                      } else {
                        output$menu_screening <- renderMenu(screening_menu_available)
                      }
                    }
                  } else {
                    output$menu_typing <- renderMenu(
                      sidebarMenu(
                        menuItem(
                          text = "Database",
                          tabName = "database",
                          icon = icon("hard-drive"),
                          startExpanded = TRUE,
                          menuSubItem(
                            text = "Browse Entries",
                            tabName = "db_browse_entries",
                            selected = TRUE
                          ),
                          menuSubItem(
                            text = "Scheme Info",
                            tabName = "db_schemeinfo"
                          ),
                          menuSubItem(
                            text = "Loci Info",
                            tabName = "db_loci_info"
                          ),
                          menuSubItem(
                            text = "Distance Matrix",
                            tabName = "db_distmatrix"
                          ),
                          menuSubItem(
                            text = "Missing Values",
                            tabName = "db_missing_values",
                            icon = icon("triangle-exclamation")
                          )
                        ),
                        menuItem(
                          text = "Schemes",
                          tabName = "init",
                          icon = icon("layer-group")
                        ),
                        menuItem(
                          text = "Allelic Typing",
                          tabName = "typing",
                          icon = icon("gears")
                        ),
                        menuItem(
                          text = "Visualization",
                          tabName = "visualization",
                          icon = icon("circle-nodes")
                        )
                      )
                    )
                    
                    if(!is.null(DB$scheme)) {
                      amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                       amrfinder_species = amrfinder_species)
                      
                      if(!isFALSE(amrfinder_available)) {
                        
                        output$menu_screening <- renderMenu(screening_menu_available)
                        
                      } else {
                        output$menu_screening <- renderMenu(screening_menu_available)
                      }
                    }
                  }
                  
                  # Render custom variable display
                  output$show_cust_var <- renderDataTable(
                    DB$cust_var,
                    selection = "single",
                    rownames = FALSE, 
                    options = list(
                      pageLength = 10,
                      lengthMenu = list(c(10), c('10')),  
                      columnDefs = list(list(searchable = TRUE, targets = "_all")),
                      initComplete = DT::JS(
                        "function(settings, json) {",
                        "$('th:first-child').css({'border-top-left-radius': '5px'});",
                        "$('th:last-child').css({'border-top-right-radius': '5px'});",
                        "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                        "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                        "}"
                      ),
                      drawCallback = DT::JS(
                        "function(settings) {",
                        "$('th:first-child').css({'border-top-left-radius': '5px'});",
                        "$('th:last-child').css({'border-top-right-radius': '5px'});",
                        "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                        "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                        "}"
                      )
                    )
                  )
                  
                  # Render missing values sidebar elements
                  output$missing_values_sidebar <- renderUI({
                    column(
                      width = 12,
                      fluidRow(
                        column(
                          width = 12,
                          br(),
                          materialSwitch(
                            "miss_val_height",
                            h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                            value = FALSE,
                            right = TRUE
                          )
                        ),
                        br()
                      )
                    )
                  })
                  
                  # Render scheme info download button
                  output$download_loci <- renderUI({
                    if (!is.null(DB$loci_info)) {
                      column(
                        12,
                        downloadBttn(
                          "download_loci_info",
                          style = "simple",
                          label = "",
                          size = "sm",
                          icon = icon("download"),
                          color = "primary"
                        ),
                        bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "bottom", trigger = "hover")
                      )
                    } else {NULL}
                  })
                  
                  # Render scheme info download button
                  output$download_scheme_info <- renderUI({
                    column(
                      12,
                      downloadBttn(
                        "download_schemeinfo",
                        style = "simple",
                        label = "",
                        size = "sm",
                        icon = icon("download"),
                        color = "primary"
                      ),
                      bsTooltip("download_schemeinfo_bttn", HTML("Save scheme information"), placement = "bottom", trigger = "hover")
                    )
                  })
                  
                  # Render select input to choose displayed loci
                  output$compare_select <- renderUI({
                    
                    if(nrow(DB$data) == 1) {
                      HTML(
                        paste(
                          tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to compare")
                        )
                      )
                    } else {
                      if(!is.null(input$compare_difference)) {
                        if (isFALSE(input$compare_difference)) {
                          div(
                            class = "compare-select",
                            pickerInput(
                              inputId = "compare_select",
                              label = "",
                              width = "85%",
                              choices = names(DB$allelic_profile),
                              selected = names(DB$allelic_profile)[1:20],
                              options = list(
                                `live-search` = TRUE,
                                `actions-box` = TRUE,
                                size = 10,
                                style = "background-color: white; border-radius: 5px;"
                              ),
                              multiple = TRUE
                            )
                          )
                        } else {
                          div(
                            class = "compare-select",
                            pickerInput(
                              inputId = "compare_select",
                              label = "",
                              width = "85%",
                              choices = names(DB$allelic_profile),
                              selected = names(DB$allelic_profile)[var_alleles(DB$allelic_profile)],
                              options = list(
                                `live-search` = TRUE,
                                `actions-box` = TRUE,
                                size = 10,
                                style = "background-color: white; border-radius: 5px;"
                              ),
                              multiple = TRUE
                            )
                          )
                        }
                      }
                    }
                  })
                  
                  ##### Render Entry Data Table ----
                  output$db_entries_table <- renderUI({
                    if(!is.null(DB$data)) {
                      if(between(nrow(DB$data), 1, 30)) {
                        fluidRow(
                          column(
                            width = 12,
                            rHandsontableOutput("db_entries")
                          ),
                          br(), br(),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-blue" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-orange" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-red" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-green" 
                                )
                              ),
                              column(
                                width = 9,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
                                    )
                                  )
                                )
                              )
                            )
                          )
                        )
                      } else {
                        fluidRow(
                          column(
                            width = 12,
                            rHandsontableOutput("db_entries")
                          ),
                          br(),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-blue" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-orange" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-red" 
                                )
                              ),
                              column(
                                width = 7,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
                                    )
                                  )
                                )
                              )
                            )
                          ),
                          column(
                            width = 3,
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                div(
                                  class = "rectangle-green" 
                                )
                              ),
                              column(
                                width = 9,
                                p(
                                  HTML(
                                    paste(
                                      tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
                                    )
                                  )
                                )
                              )
                            )
                          )
                        )
                      }
                    }
                  })
                  
                  if (!is.null(DB$data)) {
                    
                    
                    observe({
                      
                      if (!is.null(DB$data)) {
                        if (nrow(DB$data) == 1) {
                          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                            output$db_entries <- renderRHandsontable({
                              
                              rhandsontable(
                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
                                error_highlight = err_thresh() - 1,                              
                                rowHeaders = NULL,
                                contextMenu = FALSE,
                                highlightCol = TRUE, 
                                highlightRow = TRUE
                              ) %>%
                                hot_col(1, 
                                        valign = "htMiddle",
                                        halign = "htCenter") %>%
                                hot_col(3, readOnly = TRUE) %>%
                                hot_col(c(1, 5, 10, 11, 12, 13),
                                        readOnly = TRUE) %>%
                                hot_col(3:(13 + nrow(DB$cust_var)), 
                                        valign = "htMiddle",
                                        halign = "htLeft") %>%
                                hot_col(3, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                hot_col(4, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                hot_col(8, type = "dropdown", source = country_names) %>%
                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                                        validator = "
                                  function (value, callback) {
                                    var today_date = new Date();
                                    today_date.setHours(0, 0, 0, 0);
                                    
                                    var new_date = new Date(value);
                                    new_date.setHours(0, 0, 0, 0);
                                    
                                    try {
                                      if (new_date <= today_date) {
                                        callback(true);
                                        Shiny.setInputValue('invalid_date', false);
                                      } else {
                                        callback(false); 
                                        Shiny.setInputValue('invalid_date', true);
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  }") %>%
                                hot_cols(fixedColumnsLeft = 1) %>%
                                hot_col(2, type = "checkbox", width = "auto",
                                        valign = "htTop",
                                        halign = "htCenter") %>%
                                hot_rows(fixedRowsTop = 0) %>%
                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                             Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                             if (instance.params) {
                                                               hrows = instance.params.error_highlight
                                                               hrows = hrows instanceof Array ? hrows : [hrows]
                                                               if (hrows.includes(row)) { 
                                                                 td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
                                                               }
                                                             }
                                                         }") 
                            })
                          }
                        } else if (between(nrow(DB$data), 2, 40)) {
                          if (length(input$compare_select) > 0) {
                            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                              output$db_entries <- renderRHandsontable({
                                
                                if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                                  
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                                  w$show()
                                    
                                  entry_data <- DB$data %>%
                                    select(1:(13 + nrow(DB$cust_var))) %>%
                                    add_column(select(DB$allelic_profile_trunc, any_of(input$compare_select)))
                                  
                                  tab <- rhandsontable(
                                    entry_data,
                                    col_highlight = diff_allele() - 1,
                                    dup_names_high = duplicated_names() - 1,
                                    dup_ids_high = duplicated_ids() - 1,
                                    row_highlight = true_rows() - 1,
                                    error_highlight = err_thresh() - 1,
                                    rowHeaders = NULL,
                                    highlightCol = TRUE,
                                    highlightRow = TRUE,
                                    contextMenu = FALSE,
                                    height = entry_table_height()
                                  ) %>%
                                    hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                                            valign = "htMiddle",
                                            halign = "htCenter",
                                            readOnly = TRUE) %>%
                                    hot_col(1,
                                            valign = "htMiddle",
                                            halign = "htCenter") %>%
                                    hot_col(3, readOnly = TRUE) %>%
                                    hot_col(c(1, 5, 10, 11, 12, 13),
                                            readOnly = TRUE) %>%
                                    hot_col(3, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(4, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(3:(13 + nrow(DB$cust_var)),
                                            valign = "htMiddle",
                                            halign = "htLeft") %>%
                                    hot_col(8, type = "dropdown", source = country_names) %>%
                                    hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                                            validator = "
                                  function (value, callback) {
                                    var today_date = new Date();
                                    today_date.setHours(0, 0, 0, 0);
  
                                    var new_date = new Date(value);
                                    new_date.setHours(0, 0, 0, 0);
  
                                    try {
                                      if (new_date <= today_date) {
                                        callback(true);
                                        Shiny.setInputValue('invalid_date', false);
                                      } else {
                                        callback(false);
                                        Shiny.setInputValue('invalid_date', true);
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false);
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  }") %>%
                                    hot_col(2, type = "checkbox", width = "auto",
                                            valign = "htTop",
                                            halign = "htCenter",
                                            strict = TRUE,
                                            allowInvalid = FALSE,
                                            copyable = TRUE) %>%
                                    hot_cols(fixedColumnsLeft = 1) %>%
                                    hot_rows(fixedRowsTop = 0) %>%
                                    hot_col(1, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                         if (instance.params) {
                           hrows = instance.params.row_highlight
                           hrows = hrows instanceof Array ? hrows : [hrows]
  
                           if (hrows.includes(row)) {
                             td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)'
                           }
  
                         }
                }") %>%
                                    hot_col(diff_allele(),
                                            renderer = "
                    function(instance, td, row, col, prop, value, cellProperties) {
                      Handsontable.renderers.NumericRenderer.apply(this, arguments);
  
                      if (instance.params) {
                            hcols = instance.params.col_highlight;
                            hcols = hcols instanceof Array ? hcols : [hcols];
                          }
  
                      if (instance.params && hcols.includes(col)) {
                        td.style.background = 'rgb(116, 188, 139)';
                      }
                  }"
                                    ) %>%
                                    hot_col(4, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                         if (instance.params) {
                           hrows = instance.params.dup_names_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
  
                           if (hrows.includes(row)) {
                             td.style.backgroundColor = 'rgb(224, 179, 0)'
                           }
                         }
                }") %>%
                                    hot_col(3, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                         if (instance.params) {
                           hrows = instance.params.dup_ids_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
  
                           if (hrows.includes(row)) {
                             td.style.backgroundColor = 'rgb(224, 179, 0)'
                           }
                         }
                }") %>%
                                    hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                             Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                             if (instance.params) {
                                                               hrows = instance.params.error_highlight
                                                               hrows = hrows instanceof Array ? hrows : [hrows]
                                                               if (hrows.includes(row)) {
                                                                 td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)'
                                                               }
                                                             }
                                                         }")
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                                  return(tab)
                                }
                              })
                            }
                          } else {
                            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                              
                              output$db_entries <- renderRHandsontable({
                                
                                if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                                  w$show()
                                  
                                  tab <- rhandsontable(
                                    select(DB$data, 1:(13 + nrow(DB$cust_var))),
                                    rowHeaders = NULL,
                                    row_highlight = true_rows() - 1,
                                    dup_names_high = duplicated_names()- 1,
                                    dup_ids_high = duplicated_ids() - 1,
                                    error_highlight = err_thresh() - 1,
                                    contextMenu = FALSE,
                                    highlightCol = TRUE, 
                                    highlightRow = TRUE,
                                    height = entry_table_height()
                                  ) %>%
                                    hot_cols(fixedColumnsLeft = 1) %>%
                                    hot_col(1, 
                                            valign = "htMiddle",
                                            halign = "htCenter") %>%
                                    hot_col(3, readOnly = TRUE) %>%
                                    hot_col(c(1, 5, 10, 11, 12, 13),
                                            readOnly = TRUE) %>%
                                    hot_col(3:(13 + nrow(DB$cust_var)), 
                                            valign = "htMiddle",
                                            halign = "htLeft") %>%
                                    hot_col(3, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(4, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(8, type = "dropdown", source = country_names) %>%
                                    hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                                            validator = "
                                  function (value, callback) {
                                    var today_date = new Date();
                                    today_date.setHours(0, 0, 0, 0);
                                    
                                    var new_date = new Date(value);
                                    new_date.setHours(0, 0, 0, 0);
                                    
                                    try {
                                      if (new_date <= today_date) {
                                        callback(true);
                                        Shiny.setInputValue('invalid_date', false);
                                      } else {
                                        callback(false); 
                                        Shiny.setInputValue('invalid_date', true);
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  }") %>%
                                    hot_col(2, type = "checkbox", width = "auto",
                                            valign = "htTop",
                                            halign = "htCenter") %>%
                                    hot_rows(fixedRowsTop = 0) %>%
                                    hot_col(1, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
    
                         if (instance.params) {
                           hrows = instance.params.row_highlight
                           hrows = hrows instanceof Array ? hrows : [hrows]
    
                           if (hrows.includes(row)) { 
                             td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                           }
    
                         }
                }") %>%
                                    hot_col(4, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
    
                         if (instance.params) {
                           hrows = instance.params.dup_names_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
    
                           if (hrows.includes(row)) { 
                             td.style.backgroundColor = 'rgb(224, 179, 0)' 
                           }
                         }
                }") %>%
                                    hot_col(3, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
    
                         if (instance.params) {
                           hrows = instance.params.dup_ids_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
    
                           if (hrows.includes(row)) { 
                             td.style.backgroundColor = 'rgb(224, 179, 0)' 
                           }
                         }
                }") %>%
                                    hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                             Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                             if (instance.params) {
                                                               hrows = instance.params.error_highlight
                                                               hrows = hrows instanceof Array ? hrows : [hrows]
                                                               if (hrows.includes(row)) { 
                                                                 td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                               }
                                                             }
                                                         }") 
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                                  return(tab)
                                }
                              })
                            }
                          }
                        } else {
                          if (length(input$compare_select) > 0) {
                            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                              output$db_entries <- renderRHandsontable({
                                
                                if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                                  
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                                  w$show()
                                  
                                  entry_data <- DB$data %>%
                                    select(1:(13 + nrow(DB$cust_var))) %>%
                                    add_column(select(DB$allelic_profile_trunc, any_of(input$compare_select)))
                                  
                                  tab <- rhandsontable(
                                    entry_data,
                                    col_highlight = diff_allele() - 1,
                                    rowHeaders = NULL,
                                    height = entry_table_height(),
                                    row_highlight = true_rows() - 1,
                                    dup_names_high = duplicated_names() - 1,
                                    dup_ids_high = duplicated_ids() - 1,
                                    error_highlight = err_thresh() - 1,
                                    contextMenu = FALSE,
                                    highlightCol = TRUE,
                                    highlightRow = TRUE
                                  ) %>%
                                    hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                                            readOnly = TRUE,
                                            valign = "htMiddle",
                                            halign = "htCenter") %>%
                                    hot_col(3:(13 + nrow(DB$cust_var)),
                                            valign = "htMiddle",
                                            halign = "htLeft") %>%
                                    hot_col(3, readOnly = TRUE) %>%
                                    hot_col(3, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(4, validator = "
                                    function(value, callback) {
                                      try {
                                        if (value === null || value.trim() === '') {
                                          callback(false); // Cell is empty
                                          Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                        } else {
                                          callback(true); // Cell is not empty
                                          Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); // In case of error, consider it as invalid
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      }
                                    }
                                  ") %>%
                                    hot_col(c(1, 5, 10, 11, 12, 13),
                                            readOnly = TRUE) %>%
                                    hot_col(8, type = "dropdown", source = country_names) %>%
                                    hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                                            validator = "
                                  function (value, callback) {
                                    var today_date = new Date();
                                    today_date.setHours(0, 0, 0, 0);
  
                                    var new_date = new Date(value);
                                    new_date.setHours(0, 0, 0, 0);
  
                                    try {
                                      if (new_date <= today_date) {
                                        callback(true);
                                        Shiny.setInputValue('invalid_date', false);
                                      } else {
                                        callback(false);
                                        Shiny.setInputValue('invalid_date', true);
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false);
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  }") %>%
                                    hot_col(1,
                                            valign = "htMiddle",
                                            halign = "htCenter") %>%
                                    hot_col(2, type = "checkbox", width = "auto",
                                            valign = "htTop",
                                            halign = "htCenter",
                                            allowInvalid = FALSE,
                                            copyable = TRUE) %>%
                                    hot_cols(fixedColumnsLeft = 1) %>%
                                    hot_rows(fixedRowsTop = 0) %>%
                                    hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                             Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                             if (instance.params) {
                                                               hrows = instance.params.row_highlight
                                                               hrows = hrows instanceof Array ? hrows : [hrows]
                                                               if (hrows.includes(row)) {
                                                                 td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)'
                                                               }
                                                             }
                                                         }") %>%
                                    hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                             Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                             if (instance.params) {
                                                               hrows = instance.params.error_highlight
                                                               hrows = hrows instanceof Array ? hrows : [hrows]
                                                               if (hrows.includes(row)) {
                                                                 td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)'
                                                               }
                                                             }
                                                         }") %>%
                                    hot_col(4, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                         if (instance.params) {
                           hrows = instance.params.dup_names_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
  
                           if (hrows.includes(row)) {
                             td.style.backgroundColor = 'rgb(224, 179, 0)'
                           }
                         }
                }") %>%
                                    hot_col(3, renderer = "
                function (instance, td, row, col, prop, value, cellProperties) {
                         Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                         if (instance.params) {
                           hrows = instance.params.dup_ids_high
                           hrows = hrows instanceof Array ? hrows : [hrows]
  
                           if (hrows.includes(row)) {
                             td.style.backgroundColor = 'rgb(224, 179, 0)'
                           }
                         }
                }") %>%
                                    hot_col(diff_allele(),
                                            renderer = "
                    function(instance, td, row, col, prop, value, cellProperties) {
                      Handsontable.renderers.NumericRenderer.apply(this, arguments);
  
                      if (instance.params) {
                            hcols = instance.params.col_highlight;
                            hcols = hcols instanceof Array ? hcols : [hcols];
                          }
  
                      if (instance.params && hcols.includes(col)) {
                        td.style.background = 'rgb(116, 188, 139)';
                      }
                  }")
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')    
                                  return(tab)
                                }
                              })
                            }
                          } else {
                            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                              output$db_entries <- renderRHandsontable({
                                
                                if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                                  w$show()
                                  
                                  tab <- rhandsontable(
                                    select(DB$data, 1:(13 + nrow(DB$cust_var))),
                                    rowHeaders = NULL,
                                    height = entry_table_height(),
                                    dup_names_high = duplicated_names() - 1,
                                    dup_ids_high = duplicated_ids() - 1,
                                    row_highlight = true_rows() - 1,
                                    error_highlight = err_thresh() - 1,
                                    contextMenu = FALSE,
                                    highlightCol = TRUE, 
                                    highlightRow = TRUE
                                  ) %>%
                                    hot_cols(fixedColumnsLeft = 1) %>%
                                    hot_col(1, 
                                            valign = "htMiddle",
                                            halign = "htCenter") %>%
                                    hot_col(3, readOnly = TRUE) %>%
                                    hot_col(c(1, 5, 10, 11, 12, 13),
                                            readOnly = TRUE) %>%
                                    hot_col(3, validator = "
                                      function(value, callback) {
                                        try {
                                          if (value === null || value.trim() === '') {
                                            callback(false); // Cell is empty
                                            Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                          } else {
                                            callback(true); // Cell is not empty
                                            Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                          }
                                        } catch (err) {
                                          console.log(err);
                                          callback(false); // In case of error, consider it as invalid
                                          Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                        }
                                      }
                                    ") %>%
                                    hot_col(4, validator = "
                                      function(value, callback) {
                                        try {
                                          if (value === null || value.trim() === '') {
                                            callback(false); // Cell is empty
                                            Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                          } else {
                                            callback(true); // Cell is not empty
                                            Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                          }
                                        } catch (err) {
                                          console.log(err);
                                          callback(false); // In case of error, consider it as invalid
                                          Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                        }
                                      }
                                    ") %>%
                                    hot_col(8, type = "dropdown", source = country_names) %>%
                                    hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                                            validator = "
                                    function (value, callback) {
                                      var today_date = new Date();
                                      today_date.setHours(0, 0, 0, 0);
                                      
                                      var new_date = new Date(value);
                                      new_date.setHours(0, 0, 0, 0);
                                      
                                      try {
                                        if (new_date <= today_date) {
                                          callback(true);
                                          Shiny.setInputValue('invalid_date', false);
                                        } else {
                                          callback(false); 
                                          Shiny.setInputValue('invalid_date', true);
                                        }
                                      } catch (err) {
                                        console.log(err);
                                        callback(false); 
                                        Shiny.setInputValue('invalid_date', true);
                                      }
                                    }") %>%
                                    hot_col(3:(13 + nrow(DB$cust_var)), 
                                            valign = "htMiddle",
                                            halign = "htLeft") %>%
                                    hot_rows(fixedRowsTop = 0) %>%
                                    hot_col(1, renderer = "
                  function (instance, td, row, col, prop, value, cellProperties) {
                           Handsontable.renderers.TextRenderer.apply(this, arguments);
      
                           if (instance.params) {
                             hrows = instance.params.row_highlight
                             hrows = hrows instanceof Array ? hrows : [hrows]
      
                             if (hrows.includes(row)) { 
                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                             }
                           }
                  }") %>%
                                    hot_col(2, type = "checkbox", width = "auto",
                                            valign = "htTop", halign = "htCenter") %>%
                                    hot_col(4, renderer = "
                  function (instance, td, row, col, prop, value, cellProperties) {
                           Handsontable.renderers.TextRenderer.apply(this, arguments);
      
                           if (instance.params) {
                             hrows = instance.params.dup_names_high
                             hrows = hrows instanceof Array ? hrows : [hrows]
      
                             if (hrows.includes(row)) { 
                               td.style.backgroundColor = 'rgb(224, 179, 0)' 
                             }
                           }
                  }") %>%
                                    hot_col(3, renderer = "
                  function (instance, td, row, col, prop, value, cellProperties) {
                           Handsontable.renderers.TextRenderer.apply(this, arguments);
      
                           if (instance.params) {
                             hrows = instance.params.dup_ids_high
                             hrows = hrows instanceof Array ? hrows : [hrows]
      
                             if (hrows.includes(row)) { 
                               td.style.backgroundColor = 'rgb(224, 179, 0)' 
                             }
                           }
                  }") %>%
                                    hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                               Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                               if (instance.params) {
                                                                 hrows = instance.params.error_highlight
                                                                 hrows = hrows instanceof Array ? hrows : [hrows]
                                                                 if (hrows.includes(row)) { 
                                                                   td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                                 }
                                                               }
                                                           }") 
                                  
                                  shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                                  return(tab)  
                                }
                              })
                            }
                          }
                        }
                      }
                      
                      # Dynamic save button when rhandsontable changes or new entries
                      output$edit_entry_table <- renderUI({
                        
                        check_new_entry <- check_new_entry()
                        
                        if(!is.null(check_new_entry) & 
                           !is.null(DB$check_new_entries) & 
                           !is.null(DB$meta)) {
                          
                          if(!is.null(DB$meta)) {
                            new_meta <- !identical(get.entry.table.meta(), select(DB$meta, -13))
                          } else {
                            new_meta <- FALSE
                          }
                          
                          if(check_new_entry & DB$check_new_entries) {
                            Typing$reload <- FALSE
                            fluidRow(
                              column(
                                width = 8,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 
                                              'New entries - reload database')
                                  )
                                )
                              ),
                              column(
                                width = 4,
                                actionButton(
                                  "load",
                                  "",
                                  icon = icon("rotate"),
                                  class = "pulsating-button",
                                  width = "40px"
                                )
                              )
                            )
                          } else if(Typing$status == "Attaching") {
                            fluidRow(
                              column(
                                width = 11,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 'No database changes possible - pending entry addition')
                                  )
                                )
                              ),
                              column(
                                width = 1,
                                HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
                              )
                            )
                          } else if(isTRUE(DB$change) | new_meta) {
                            
                            if(!is.null(input$db_entries)) {
                              fluidRow(
                                column(
                                  width = 5,
                                  HTML(
                                    paste(
                                      tags$span(style='color: white; font-size: 16px; position: absolute; bottom: -30px; right: -5px', 'Confirm changes')
                                    )
                                  )
                                ),
                                column(
                                  width = 3,
                                  actionButton(
                                    "edit_button",
                                    "",
                                    icon = icon("bookmark"),
                                    class = "pulsating-button"
                                  )
                                ),
                                column(
                                  width = 4,
                                  actionButton(
                                    "undo_changes",
                                    "Undo",
                                    icon = icon("repeat")
                                  )
                                )
                              )
                            }
                          } else {NULL}
                        }
                      })
                    })
                    
                    # Hide no entry message
                    output$db_no_entries <- NULL
                    output$distancematrix_no_entries <- NULL
                    
                  } else {
                    
                    # If database loading not successful dont show entry table
                    output$db_entries_table <- NULL
                    output$entry_table_controls <- NULL
                  }
                  
                  # Render Entry table controls
                  output$entry_table_controls <- renderUI({
                    fluidRow(
                      column(
                        width = 4,
                        align = "center",
                        fluidRow(
                          column(
                            width = 4,
                            align = "center",
                            actionButton(
                              "sel_all_entries",
                              "Select All",
                              icon = icon("check")
                            )
                          ),
                          column(
                            width = 4,
                            align = "left",
                            actionButton(
                              "desel_all_entries",
                              "Deselect All",
                              icon = icon("xmark")
                            )
                          )
                        )
                      ),
                      column(
                        width = 3,
                        uiOutput("edit_entry_table")
                      )
                    )
                  })
                  
                  ## Render Distance Matrix ----
                  observe({
                    if(!is.null(DB$data)) {
                      shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                      
                      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
                        output$db_distancematrix <- NULL
                        
                        if( (sum(duplicated(DB$meta$`Assembly Name`)) > 0) & (sum(duplicated(DB$meta$`Assembly ID`)) == 0) ) {
                          duplicated_txt <- paste0(
                            paste(
                              paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
                              DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
                            ),
                            "<br>"
                          )
                        } else if ( (sum(duplicated(DB$meta$`Assembly ID`)) > 0) & (sum(duplicated(DB$meta$`Assembly Name`)) == 0) ){
                          duplicated_txt <- paste0(
                            paste(
                              paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
                              DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
                            ),
                            "<br>"
                          )
                        } else {
                          duplicated_txt <- c(
                            paste0(
                              paste(
                                paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
                                DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
                              ),
                              "<br>"
                            ),
                            paste0(
                              paste(
                                paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
                                DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
                              ),
                              "<br>"
                            )
                          )
                        }
                        
                        output$distancematrix_duplicated <- renderUI({
                          column(
                            width = 12,
                            tags$span(style = "font-size: 15; color: white",
                                      "Change duplicated entry names to display distance matrix."),
                            br(), br(), br(),
                            actionButton("change_entries", "Go to Entry Table", class = "btn btn-default"),
                            br(), br(), br(),
                            tags$span(
                              style = "font-size: 15; color: white",
                              HTML(
                                append(
                                  "Duplicated:",
                                  append(
                                    "<br>",
                                    duplicated_txt
                                  )
                                )
                              )
                            )
                          )
                        })
                      } else {
                        output$distancematrix_duplicated <- NULL
                        if(!is.null(DB$data) & !is.null(DB$allelic_profile) & !is.null(DB$allelic_profile_true) & !is.null(DB$cust_var) & !is.null(input$distmatrix_label) & !is.null(input$distmatrix_diag) & !is.null(input$distmatrix_triangle)) {
                          dist_matrix <- hamming_df()
                          
                          req(dist_matrix)
                          
                          output$db_distancematrix <- renderRHandsontable({
                            
                            if(nrow(dist_matrix) > 28) {
                              height <- 700
                            } else {
                              height <- NULL
                            }
                            
                            rhandsontable(dist_matrix, 
                                          digits = 1, 
                                          readOnly = TRUE,
                                          contextMenu = FALSE,
                                          highlightCol = TRUE, 
                                          highlightRow = TRUE,
                                          height = height, 
                                          rowHeaders = NULL) %>%
                              hot_heatmap(renderer = paste0("
                              function (instance, td, row, col, prop, value, cellProperties) {
                                Handsontable.renderers.TextRenderer.apply(this, arguments);
                                heatmapScale  = chroma.scale(['#17F556', '#ED6D47']);
                              
                                if (instance.heatmap[col]) {
                                  mn = ", DB$matrix_min, ";
                                  mx = ", DB$matrix_max, ";
                              
                                  pt = (parseInt(value, 10) - mn) / (mx - mn);    
                              
                                  td.style.backgroundColor = heatmapScale(pt).hex();
                                }
                              }")) %>%
                              hot_rows(fixedRowsTop = 0) %>%
                              hot_cols(fixedColumnsLeft = 1) %>%
                              hot_col(1:(dim(dist_matrix)[1]+1),
                                      halign = "htCenter",
                                      valign = "htMiddle") %>%
                              hot_col(1, renderer = "
                              function(instance, td, row, col, prop, value, cellProperties) {
                                Handsontable.renderers.NumericRenderer.apply(this, arguments);
                                td.style.background = '#F0F0F0'
                              }"
                              )
                          })  
                        }
                      }
                      
                      # Render Distance Matrix UI
                      
                      output$distmatrix_show <- renderUI({
                        if(!is.null(DB$data)) {
                          if(nrow(DB$data) > 1) {
                            
                            if(!is.null(input$distmatrix_label)) {
                              distmatrix_label_selected <- input$distmatrix_label
                            } else {
                              distmatrix_label_selected <- c("Assembly Name")
                            }
                            
                            if(!is.null(input$distmatrix_true)) {
                              distmatrix_true_selected <- input$distmatrix_true
                            } else {
                              distmatrix_true_selected <- FALSE
                            }
                            
                            if(!is.null(input$distmatrix_triangle)) {
                              distmatrix_triangle_selected <- input$distmatrix_triangle
                            } else {
                              distmatrix_triangle_selected <- FALSE
                            }
                            
                            if(!is.null(input$distmatrix_diag)) {
                              distmatrix_diag_selected <- input$distmatrix_diag
                            } else {
                              distmatrix_diag_selected <- TRUE
                            }
                            
                            fluidRow(
                              column(1),
                              div(
                                class = "distancematrix-options",
                                column(
                                  width = 2,
                                  box(
                                    solidHeader = TRUE,
                                    status = "primary",
                                    width = "100%",
                                    title = "Options",
                                    column(
                                      width = 12,
                                      br(),
                                      br(),
                                      fluidRow(
                                        column(
                                          width = 3,
                                          HTML(
                                            paste(
                                              tags$span(style='color: white; font-size: 14px;', 
                                                        'Label')
                                            )
                                          )
                                        ),
                                        column(
                                          width = 9,
                                          div(
                                            class = "distmatrix-label",
                                            selectInput(
                                              "distmatrix_label",
                                              label = "",
                                              choices = c("Index", "Assembly Name", "Assembly ID"),
                                              selected = distmatrix_label_selected,
                                              width = "100%"
                                            )
                                          )
                                        )
                                      ),
                                      br(),
                                      br(),
                                      div(
                                        class = "mat-switch-dmatrix",
                                        materialSwitch(
                                          "distmatrix_true",
                                          h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                          value = distmatrix_true_selected,
                                          right = TRUE
                                        )
                                      ),
                                      br(),
                                      div(
                                        class = "mat-switch-dmatrix",
                                        materialSwitch(
                                          "distmatrix_triangle",
                                          h5(p("Show Upper Triangle"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                          value = distmatrix_triangle_selected,
                                          right = TRUE
                                        )
                                      ),
                                      br(),
                                      div(
                                        class = "mat-switch-dmatrix",
                                        materialSwitch(
                                          "distmatrix_diag",
                                          h5(p("Show Diagonal"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                          value = distmatrix_diag_selected,
                                          right = TRUE
                                        )
                                      ),
                                      br(),
                                      br(),
                                      br(),
                                      br(),
                                      fluidRow(
                                        column(
                                          width = 8,
                                          HTML(
                                            paste(
                                              tags$span(style='color: white; font-size: 14px;', 
                                                        'Download CSV')
                                            )
                                          )
                                        ),
                                        column(
                                          width = 4,
                                          downloadBttn(
                                            "download_distmatrix",
                                            style = "simple",
                                            label = "",
                                            size = "sm",
                                            icon = icon("download")
                                          )
                                        )
                                      )
                                    )
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                uiOutput("distancematrix_duplicated"),
                                rHandsontableOutput("db_distancematrix")
                              )
                            )
                          } else {
                            column(
                              width = 9,
                              align = "left",
                              p(
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to display a distance matrix.")
                                  )
                                )
                              ),
                              br(),
                              br()
                            )
                          }
                        }
                      })
                      shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                    }
                  })
                  
                  # render custom variables box UI
                  output$custom_var_box <- renderUI(
                    box(
                      solidHeader = TRUE,
                      status = "primary",
                      width = "100%",
                      title = "Custom Variables",
                      fluidRow(
                        column(1),
                        column(
                          width = 7,
                          fluidRow(
                            column(
                              width = 9,
                              align = "center",
                              textInput(
                                "new_var_name",
                                label = "",
                                placeholder = "New Variable"
                              )
                            ),
                            column(
                              width = 2,
                              actionButton(
                                "add_new_variable",
                                "",
                                icon = icon("plus")
                              )
                            )
                          ),
                          fluidRow(
                            column(
                              width = 9,
                              align = "center",
                              selectInput(
                                "del_which_var",
                                "",
                                DB$cust_var$Variable
                              )
                            ),
                            column(
                              width = 2,
                              align = "left",
                              actionButton(
                                "delete_new_variable",
                                "",
                                icon = icon("minus")
                              )
                            )
                          )   
                        ),
                        column(
                          width = 2,
                          actionButton(
                            "custom_var_table",
                            "Browse ",
                            icon = icon("table-list")
                          )
                        )
                      )
                    )
                  )
                  
                  # Render delete entry box UI
                  output$delete_box <- renderUI({
                    box(
                      solidHeader = TRUE,
                      status = "primary",
                      width = "100%",
                      title = "Delete Entries",
                      fluidRow(
                        column(1),
                        column(
                          width = 5,
                          align = "left",
                          uiOutput("delete_select")
                        ),
                        column(
                          width = 2,
                          align = "center",
                          br(),
                          uiOutput("del_bttn")
                        )
                      ),
                      br()
                    )
                  })
                  
                  # Render loci comparison box UI
                  output$compare_allele_box <- renderUI({
                    box(
                      solidHeader = TRUE,
                      status = "primary",
                      width = "100%",
                      title = "Compare Loci",
                      column(
                        width = 12,
                        br(),
                        fluidRow(
                          column(1),
                          column(
                            width = 10,
                            align = "left",
                            uiOutput("compare_select")   
                          )
                        ),
                        br(),
                        fluidRow(
                          column(1),
                          column(
                            width = 10,
                            align = "left",
                            uiOutput("compare_difference_box")
                          )
                        )
                      ),
                      br()
                    )
                  })
                  
                  # Render entry table download box UI
                  output$download_entries <- renderUI({
                    fluidRow(
                      column(
                        width = 12,
                        box(
                          solidHeader = TRUE,
                          status = "primary",
                          width = "100%",
                          title = "Export Table",
                          fluidRow(
                            column(1),
                            column(
                              width = 8,
                              align = "left",
                              br(),
                              div(
                                class = "mat-switch-db",
                                materialSwitch(
                                  "download_table_include",
                                  h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                  value = FALSE,
                                  right = TRUE
                                )
                              ),
                              div(
                                class = "mat-switch-db",
                                materialSwitch(
                                  "download_table_loci",
                                  h5(p("Include Displayed Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                  value = FALSE,
                                  right = TRUE
                                )
                              ),
                              div(
                                class = "mat-switch-db",
                                materialSwitch(
                                  "download_table_hashes",
                                  h5(p("Truncate Hashes"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                                  value = FALSE,
                                  right = TRUE
                                )
                              )
                            ),
                            column(
                              width = 2,
                              align = "center",
                              downloadBttn(
                                "download_entry_table",
                                style = "simple",
                                label = "",
                                size = "sm",
                                icon = icon("download"),
                                color = "primary"
                              )
                            )
                          )
                        )
                      )
                    )
                  })
                  
                  # Render entry deletion select input
                  output$delete_select <- renderUI({
                    pickerInput("select_delete",
                                label = h5("Index", style = "color:white; margin-bottom: 0px;"),
                                choices = DB$data[, "Index"],
                                options = list(
                                  `live-search` = TRUE,
                                  `actions-box` = TRUE,
                                  size = 10,
                                  style = "background-color: white; border-radius: 5px;"
                                ),
                                multiple = TRUE)
                  })
                  
                  # Render delete entry button
                  output$del_bttn <- renderUI({
                    actionBttn(
                      "del_button",
                      label = "",
                      color = "danger",
                      size = "sm",
                      style = "material-circle",
                      icon = icon("xmark")
                    )
                  })
                  
                  # Missing Values UI ----
                  
                  # Missing values calculations and table 
                  observe({
                    if(!is.null(DB$allelic_profile)) {
                      NA_table <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) != 0]
                      
                      NA_table <- NA_table[rowSums(is.na(NA_table)) != 0,]
                      
                      NA_table[is.na(NA_table)] <- "NA"
                      
                      NA_table <- NA_table %>% 
                        cbind("Assembly Name" = DB$meta[rownames(NA_table),]$`Assembly Name`) %>%
                        cbind("Errors" = DB$meta[rownames(NA_table),]$Errors) %>%
                        relocate("Assembly Name", "Errors")
                      
                      DB$na_table <- NA_table
                      
                      output$table_missing_values <- renderRHandsontable({
                        
                        if(nrow(DB$na_table) > 26) {
                          height <- 650
                        } else {
                          height <- NULL
                        }
                        
                        rhandsontable(
                          DB$na_table,
                          readOnly = TRUE,
                          rowHeaders = NULL,
                          contextMenu = FALSE,
                          height = height,
                          highlightCol = TRUE, 
                          highlightRow = TRUE,
                          error_highlight = err_thresh_na() - 1
                        ) %>%
                          hot_cols(fixedColumnsLeft = 1) %>%
                          hot_rows(fixedRowsTop = 0) %>%
                          hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
                          hot_col(2, renderer = "
                              function (instance, td, row, col, prop, value, cellProperties) {
                                Handsontable.renderers.TextRenderer.apply(this, arguments);
                                if (instance.params) {
                                  hrows = instance.params.error_highlight
                                  hrows = hrows instanceof Array ? hrows : [hrows]
                                  if (hrows.includes(row)) { 
                                    td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
                                  }
                                }
                              }") %>%
                          hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
                            "function(instance, td, row, col, prop, value, cellProperties) {
                                  if (value.length > 8) {
                                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
                                  }
                                  td.innerHTML = value;
                                  td.style.textAlign = 'center';
                                  return td;
                                 }"
                          ))
                      })
                    }
                  })
                  
                  # Render missing value informatiojn box UI
                  output$missing_values <- renderUI({
                    box(
                      solidHeader = TRUE,
                      status = "primary",
                      width = "100%",
                      title = "Missing Value Handling",
                      fluidRow(
                        div(
                          class = "white",
                          column(
                            width = 12,
                            align = "left",
                            br(), 
                            HTML(
                              paste0("There are ", 
                                     strong(as.character(sum(is.na(DB$data)))), 
                                     " unsuccessful allele allocations (NA). ",
                                     strong(sum(sapply(DB$allelic_profile, anyNA))),
                                     " out of ",
                                     strong(ncol(DB$allelic_profile)),
                                     " total loci in this scheme contain NA's (",
                                     strong(round((sum(sapply(DB$allelic_profile, anyNA)) / ncol(DB$allelic_profile) * 100), 1)),
                                     " %). ",
                                     "<br><br><br>Decide how these missing values should be treated:")
                              
                            ),
                            br()
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 12,
                          align = "left",
                          br(),
                          div(
                            class = "na-handling",
                            prettyRadioButtons(
                              "na_handling",
                              "",
                              choiceNames = c("Ignore missing values for pairwise comparison",
                                              "Omit loci with missing values for all assemblies",
                                              "Treat missing values as allele variant"),
                              choiceValues = c("ignore_na", "omit", "category"),
                              shape = "curve",
                              selected = c("ignore_na")
                            )
                          ),
                          br()
                        )
                      )
                    )
                  })  
                  
                } else { 
                  #if no typed assemblies present
                  
                  # null underlying database
                  
                  DB$data <- NULL
                  DB$meta <- NULL
                  DB$meta_gs <- NULL
                  DB$meta_true <- NULL
                  DB$allelic_profile <- NULL
                  DB$allelic_profile_trunc <- NULL
                  DB$allelic_profile_true <- NULL
                  
                  # Render menu without missing values tab
                  output$menu_typing <- renderMenu(
                    sidebarMenu(
                      menuItem(
                        text = "Database",
                        tabName = "database",
                        icon = icon("hard-drive"),
                        startExpanded = TRUE,
                        selected = TRUE,
                        menuSubItem(
                          text = "Browse Entries",
                          tabName = "db_browse_entries"
                        ),
                        menuSubItem(
                          text = "Scheme Info",
                          tabName = "db_schemeinfo"
                        ),
                        menuSubItem(
                          text = "Loci Info",
                          tabName = "db_loci_info"
                        ),
                        menuSubItem(
                          text = "Distance Matrix",
                          tabName = "db_distmatrix"
                        )
                      ),
                      menuItem(
                        text = "Schemes",
                        tabName = "init",
                        icon = icon("layer-group")
                      ),
                      menuItem(
                        text = "Allelic Typing",
                        tabName = "typing",
                        icon = icon("gears")
                      ),
                      menuItem(
                        text = "Visualization",
                        tabName = "visualization",
                        icon = icon("circle-nodes")
                      )
                    )
                  )
                  
                  if(!is.null(DB$scheme)) {
                    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                                     amrfinder_species = amrfinder_species)
                    
                    if(!isFALSE(amrfinder_available)) {
                      
                      output$menu_screening <- renderMenu(screening_menu_available)
                      
                    } else {
                      output$menu_screening <- renderMenu(screening_menu_available)
                    }
                  }
                  
                  observe({
                    if(is.null(DB$data)) {
                      if(check_new_entry()) {
                        output$db_no_entries <- renderUI(
                          column(
                            width = 12,
                            fluidRow(
                              column(1),
                              column(
                                width = 3,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
                                  )
                                )
                              ),
                              column(
                                width = 4,
                                actionButton(
                                  "load",
                                  "",
                                  icon = icon("rotate"),
                                  class = "pulsating-button",
                                  width = "40px"
                                )
                              )
                            )
                          )
                        )
                      } else {
                        output$db_no_entries <- renderUI(
                          column(
                            width = 12,
                            fluidRow(
                              column(1),
                              column(
                                width = 11,
                                align = "left",
                                HTML(
                                  paste(
                                    "<span style='color: white;'>",
                                    "No Entries for this scheme available.\n",
                                    "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
                                    sep = '<br/>'
                                  )
                                )
                              )
                            )
                          )
                        )
                      }
                    }
                  })
                  
                  # Render scheme info download button
                  output$download_scheme_info <- renderUI({
                    column(
                      12,
                      downloadBttn(
                        "download_schemeinfo",
                        style = "simple",
                        label = "",
                        size = "sm",
                        icon = icon("download"),
                        color = "primary"
                      ),
                      bsTooltip("download_schemeinfo_bttn", HTML("Save scheme information"), placement = "bottom", trigger = "hover")
                    )
                  })
                  
                  # Render scheme info download button
                  output$download_loci <- renderUI({
                    if (!is.null(DB$loci_info)) {
                      column(
                        12,
                        downloadBttn(
                          "download_loci_info",
                          style = "simple",
                          label = "",
                          size = "sm",
                          icon = icon("download"),
                          color = "primary"
                        ),
                        bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "bottom", trigger = "hover")
                      )
                    } else {NULL}
                  })
                  
                  output$distancematrix_no_entries <- renderUI(
                    fluidRow(
                      column(1),
                      column(
                        width = 11,
                        align = "left",
                        HTML(paste(
                          "<span style='color: white;'>",
                          "No Entries for this scheme available.",
                          "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
                          sep = '<br/>'
                        ))
                      )
                    )
                  )
                  
                  output$db_entries <- NULL
                  output$edit_index <- NULL
                  output$edit_scheme_d <- NULL
                  output$edit_entries <- NULL
                  output$compare_select <- NULL
                  output$delete_select <- NULL
                  output$del_bttn <- NULL
                  output$compare_allele_box <- NULL
                  output$download_entries <- NULL
                  output$missing_values <- NULL
                  output$custom_var_box <- NULL
                  output$delete_box <- NULL
                  output$entry_table_controls <- NULL
                  output$multi_stop <- NULL
                  output$metadata_multi_box <- NULL
                  output$start_multi_typing_ui <- NULL
                  output$pending_typing <- NULL
                  output$multi_typing_results <- NULL
                  output$single_typing_progress <- NULL
                  output$metadata_single_box <- NULL
                  output$start_typing_ui <- NULL
                  
                  output$initiate_typing_ui <- renderUI({
                    column(
                      width = 4,
                      align = "center",
                      br(),
                      br(),
                      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
                      br(),
                      br(),
                      p(
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
                          )
                        )
                      ),
                      fluidRow(
                        column(1),
                        column(
                          width = 11,
                          align = "center",
                          shinyFilesButton(
                            "genome_file",
                            "Browse" ,
                            icon = icon("file"),
                            title = "Select the assembly in .fasta/.fna/.fa format:",
                            multiple = FALSE,
                            buttonType = "default",
                            class = NULL,
                            root = path_home()
                          ),
                          br(),
                          br(),
                          uiOutput("genome_path"),
                          br()
                        )
                      )
                    )
                  })
                  
                  output$initiate_typing_ui <- renderUI({
                    column(
                      width = 4,
                      align = "center",
                      br(),
                      br(),
                      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
                      br(),
                      br(),
                      p(
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
                          )
                        )
                      ),
                      fluidRow(
                        column(1),
                        column(
                          width = 11,
                          align = "center",
                          shinyFilesButton(
                            "genome_file",
                            "Browse" ,
                            icon = icon("file"),
                            title = "Select the assembly in .fasta/.fna/.fa format:",
                            multiple = FALSE,
                            buttonType = "default",
                            class = NULL,
                            root = path_home()
                          ),
                          br(),
                          br(),
                          uiOutput("genome_path"),
                          br()
                        )
                      )
                    )
                  })
                  
                  output$initiate_multi_typing_ui <- initiate_multi_typing_ui
                }
              }
            }
          }
        } else {
          
          log_print("Invalid scheme folder")
          show_toast(
            title = "Invalid scheme folder",
            type = "warning",
            position = "bottom-end",
            timer = 4000
          )
        }
      }
      
      
      ### Check if scheme update available
      if(!is.null(DB$scheme_db) && isTRUE(DB$scheme_new)) {
        
        # Query remote scheme
        if(DB$scheme_db == "cgMLST.org Nomenclature Server (h25)") {
          
          db_spec <- schemes[schemes[,"database"] == "cgMLST.org",]
          DB$url_link <- db_spec[, "url"][db_spec[, "species"] == gsub(" ", "_", DB$scheme)]
          
          remote <- tryCatch({
            read_html(DB$url_link)
          }, error = function(e) {
            DB$failCon <- TRUE
            show_toast(
              title = "Could not retrieve data. Check internet connection.",
              type = "error",
              position = "bottom-end",
              timer = 6000
            )
            warning("Could not retrieve data. Check internet connection.")
            return(NULL)
          })
          
          if(is.null(remote)) {
            last_scheme_change <- NULL
          } else {
            DB$failCon <- FALSE
            remote_scheme <- remote %>%
              html_table(header = FALSE) %>%
              as.data.frame(stringsAsFactors = FALSE)
            
            last_scheme_change <- strptime(remote_scheme[,2][remote_scheme[,1] == "Last Change"],
                                           format = "%B %d, %Y, %H:%M %p")
          }
        } else if(DB$scheme_db == "pubMLST") {
          
          db_spec <- schemes[schemes[,"database"] == "pubMLST",]
          DB$url_link <- db_spec[, "url"][db_spec[, "species"] == gsub(" ", "_", DB$scheme)]
          
          remote_scheme <- get.schemeinfo(url_link = DB$url_link)
          
          if(is.null(remote_scheme)) {
            last_scheme_change <- NULL
          } else {
            last_scheme_change <- remote_scheme[["last_updated"]]
          }
        }
        
        if(!is.null(last_scheme_change)) {
          if(length(last_scheme_change) > 0) {
            last_file_change <- format(
              file.info(file.path(Startup$database, ".downloaded_schemes",
                                  paste0(gsub(" ", "_", DB$scheme), ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
            
            if(!is.null(last_file_change)) {
              if(length(last_file_change) > 0 & length(last_scheme_change) > 0) {
                if(last_file_change < last_scheme_change) {
                  showModal(
                    div(
                      class = "start-modal",
                      modalDialog(
                        fluidRow(
                          br(), 
                          column(
                            width = 11,
                            p(
                              HTML(
                                paste0(
                                  '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                                  "The ", DB$scheme, " scheme was updated at ",
                                  last_scheme_change,
                                  " on the ",
                                  DB$schemeinfo[,2][DB$schemeinfo[,1] == "Database"],
                                  " database. To fetch the changes download the scheme.",
                                  '</span>'
                                )
                              )
                            )
                          ),
                          br()
                        ),
                        title = HTML(paste0(
                          '<i class="fa-solid fa-circle-exclamation" style="font-size:17px;color:white"></i>',
                          " &nbsp;&nbsp; Scheme update available")),
                        fade = TRUE,
                        easyClose = TRUE,
                        footer = tagList(
                          modalButton("Dismiss"),
                          actionButton("update_scheme", "Update Scheme", 
                                       icon = icon("layer-group"),
                                       class = "btn btn-default")
                        )
                      )
                    )
                  )
                }
              }
            }
          }
        }
      }
      
      DB$scheme_new <- FALSE
      
      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
      shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
      
      waiter_hide()
    }  
  })
  
  # _______________________ ####
  
  ## Database ----
  
  ### Conditional UI Elements rendering ----
  
  # Render the notification dropdown menu
  output$notificationMenu <- renderMenu({
    if (isTRUE(DB$failCon)) {
      dropdownMenu(
        type = "notifications",
        notificationItem(
          text = "Network connectivity unavailable",
          icon = icon("wifi"),
          status = "danger"
        )
      )
    } else {
      dropdownMenu(type = "notifications") 
    }
  })
  
  #### Scheme Info ----
  
  output$distance_matrix_info <- renderUI({
    req(DB$scheme)
    
    if(!is.null(DB$allelic_profile)) {
      if(anyNA(DB$allelic_profile)) {
        any_na <- TRUE
      } else {any_na <- FALSE}
    } else {any_na <- FALSE}
    
    if(!is.null(input$na_handling)) {
      na_handling <- input$na_handling
    } else {
      na_handling <- "default"
    }
    column(
      width = 7,
      align = "left",
      p(
        HTML(
          paste(
            if(isTRUE(any_na)) {
              '<span style="color: white; font-size: 13px; position:relative; top:15px;">'
            } else {
              '<span style="color: white; font-size: 14px; position:relative; top:27px;">' 
            },
            'Allelic distance according to',
            '<span style="font-style: italic;">',
            DB$scheme, '</span>', 'scheme.',
            '</span>'
          )
        )
      ),
      if(isTRUE(any_na)) {
        p(
          HTML(
            paste(
              '<i class="fa-solid fa-circle-exclamation" style="font-size:13px; color:white; position:relative; top:10px; margin-right: 10px;"></i>',
              '<span style="color:white; font-size:13px; position:relative; top:10px;">',
              'Missing value handling:',
              '</span>',
              '<span style="color:white; font-style:italic; font-size:13px; position:relative; top:10px;">',
              if(na_handling == "ignore_na") {
                "&nbsp;&nbsp;Ignore missing values for pairwise comparison" 
              } else if(na_handling == "omit") {
                "&nbsp;&nbsp;Omit loci with missing values for all assemblies"   
              } else if(na_handling == "category") {
                "&nbsp;&nbsp;Treat missing values as allele variant"
              } else {
                "&nbsp;&nbsp;Ignore missing values for pairwise comparison" 
              },
              '</span>'
            )
          )
        )
      }
    ) 
  })
  
  # Species info selector UI
  observe({
    req(DB$scheme, Startup$database)
    
    scheme_path <- file.path(Startup$database, 
                             gsub(" ", "_", DB$scheme), 
                             gsub(" ", "_", DB$scheme))
    
    if(file.exists(paste0(scheme_path, ".rds"))) {
      species_data <- readRDS(paste0(scheme_path, ".rds"))
      if(!is.null(species_data)) {
        if(length(species_data) > 1) {
          choices <- gsub(" ", "_", unlist(lapply(species_data, function(x) x$Name$name)))
          names(choices) <- gsub("_", " ", unlist(lapply(species_data, function(x) x$Name$name)))
          output$species_info_select_saved <- renderUI({
            fluidRow(
              column(1),
              column(
                width = 3,
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; font-size: 15px; position: relative; top: 26px;">',
                      'Species Complex',
                      '</span>'
                    )
                  )
                )
              ),
              column(
                width = 1,
                bslib::tooltip(
                  bsicons::bs_icon("question-circle", 
                                   title = "Scheme comprises multiple species.", 
                                   color = "white", height = "14px", width = "14px", 
                                   position = "relative", top = "9px", right = "28px"),
                  "Text shown in the tooltip.",
                  show = FALSE,
                  id = "schemeinfo_tooltip_saved"
                )
              ),
              column(
                width = 6,
                selectInput(
                  "selected_species_saved",
                  "",
                  choices = choices
                )
              )
            )
          })
        } else {
          output$species_info_select_saved <- NULL
        }
      } else {
        output$species_info_select_saved <- NULL
      }
    }
  })
  
  output$species_info_saved <- renderUI({
    req(Startup$database, DB$scheme)
    
    species_data_path <- file.path(Startup$database,
                                   gsub(" ", "_", DB$scheme),
                                   paste0(gsub(" ", "_", DB$scheme), ".rds"))
    
    if(file.exists(species_data_path)) {
      species_data <- readRDS(species_data_path)
      if(length(species_data) > 1) {
        if(!is.null(input$selected_species_saved)) {
          image_path <- file.path(Startup$database,
                                  gsub(" ", "_", DB$scheme),
                                  paste0(names(species_data)[names(species_data) == input$selected_species_saved],
                                         ".jpg"))
          
          if(file.exists(image_path)) {
            output$species_no_img_saved <- NULL
            output$species_img_saved <- renderImage({
              list(src = image_path,
                   height = 180)
            }, deleteFile = FALSE)
          } else {
            output$species_no_img_saved <- renderUI(
              HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
            )
            output$species_img_saved <- NULL
          }
        } else {
          output$species_no_img_saved <- renderUI(
            HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
          )
          output$species_img_saved <- NULL
        }
      } else if (length(species_data) > 0) {
        image_path <- file.path(Startup$database, gsub(" ", "_", DB$scheme),
                                paste0(gsub("_(PM|CM)", "", 
                                            gsub(" ", "_", DB$scheme)), ".jpg"))
        
        if(file.exists(image_path)) {
          output$species_no_img_saved <- NULL
          output$species_img_saved <- renderImage({
            list(src = image_path,
                 height = 180)
          }, deleteFile = FALSE)
        } else {
          output$species_no_img_saved <- renderUI(
            HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
          )
          output$species_img_saved <- NULL
        }
      }
      
      multiple <- length(species_data) > 1 & !is.null(input$selected_species_saved)
      if(multiple) {
        species_data <- species_data[[input$selected_species_saved]]
      } else {
        species_data <- species_data[[1]]
      }
      
      if(!is.null(species_data)) {
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = HTML(
            paste0(
              '<span style="color: white; font-size: 15px;">',
              'Species Information - Data Fetched from NCBI&nbsp&nbsp&nbsp ',
              ' <a href="', 'https://www.ncbi.nlm.nih.gov/' , '" target="_blank" style="color:#008edb; font-style:normal; text-decoration:none;"> https://www.ncbi.nlm.nih.gov/ </a>',
              '</span>'
            )
          ),
          column(
            width = 12,
            fluidRow(
              br(),
              column(
                width = 7,
                p(
                  HTML(
                    paste0(
                      '<i class="fa-solid fa-bacterium" style="font-size:20px;color:white; margin-right: 10px;"></i>',
                      '<span style="color: white; font-size: 22px; ">',
                      species_data$Name$name,
                      '</span>'
                    )
                  )
                ),
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; font-size: 12px;">',
                      species_data$Name$authority,
                      '</span>'
                    )
                  )
                ),
                br(),
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; font-size: 15px;">',
                      'URL: ',
                      '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                      species_data$ID,
                      '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                      species_data$Name$name,
                      ' NCBI',
                      '</a>',
                      '</span>'
                    )
                  )
                ),
                br(),
                fluidRow(
                  column(
                    width = 12,
                    p(
                      HTML(
                        paste0(
                          '<span style="color: white; font-size: 20px;">',
                          'Lineage', '</span>'
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$superkingdom$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$superkingdom$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        align = "left",
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Superkingdom',
                              '</span>'
                            )
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$phylum$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$phylum$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Phylum',
                              '</span>'
                            )
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$class$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$class$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        align = "left",
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Class',
                              '</span>'
                            )
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$order$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$order$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        align = "left",
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Order',
                              '</span>'
                            )
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$family$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$family$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        align = "left",
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Family',
                              '</span>'
                            )
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 6,
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 15px;">',
                              '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                              species_data$Classification$genus$id,
                              '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                              species_data$Classification$genus$name,
                              '</a>',
                              '</span>'
                            )
                          )
                        )
                      ),
                      column(
                        width = 6,
                        align = "left",
                        p(
                          HTML(
                            paste0(
                              '<span style="color: white; font-size: 12px;">',
                              'Genus',
                              '</span>'
                            )
                          )
                        )
                      )
                    )
                  )
                )
              ),
              column(
                width = 5,
                align = "right",
                uiOutput("species_no_img_saved"),
                div(
                  class = "species-image",
                  imageOutput("species_img_saved", width = "300px", height = "200px")
                ),
                
              )
            )
          )
        )
      } else {NULL}
    }
  })
  
  # Scheme selector UI 
  output$scheme_selector <- renderUI({
    if(!is.null(DB$scheme)) {
      scheme_names <- schemes$species
      names(scheme_names) <- ifelse(scheme_names %in% gsub(" ", "_", DB$available),
                                    paste(scheme_names, "\U1F5BF"),
                                    scheme_names)
      
      div(
        class = "select-cgmlst",
        pickerInput(
          inputId = "select_cgmlst",
          label = NULL,
          choices = scheme_names,
          choicesOpt = list(
            subtext = paste("Database", 
                            schemes$database,
                            sep = ": ")),
          width = "auto",
          selected = gsub(" ", "_", DB$scheme),
          options = list(
            `live-search` = TRUE,
            `actions-box` = TRUE,
            size = 10,
            style = "background-color: white; border-radius: 5px;"
          ),
          multiple = FALSE
        )
      )
    } else {
      pickerInput(
        inputId = "select_cgmlst",
        label = NULL,
        choices = schemes$species,
        choicesOpt = list(
          subtext = paste("Database", 
                          schemes$database,
                          sep = ": ")),
        width = "300px",
        selected = NULL,
        options = list(
          `live-search` = TRUE,
          `actions-box` = TRUE,
          size = 10,
          style = "background-color: white; border-radius: 5px;"
        ),
        multiple = FALSE
      )
    }
  })
  
  # Control custom variables table
  output$cust_var_select <- renderUI({
    if(nrow(DB$cust_var) > 5) {
      selectInput(
        "cust_var_select",
        "",
        choices = 1:ceiling(nrow(DB$cust_var) / 5 )
      )
    }
  })
  
  output$cust_var_info <- renderUI({
    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
      if(nrow(DB$cust_var) > 5) {
        low <- -4
        high <- 0
        for (i in 1:input$cust_var_select) {
          low <- low + 5
          if((nrow(DB$cust_var) %% 5) != 0) {
            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
              high <- high + nrow(DB$cust_var) %% 5
            } else {
              high <- high + 5
            }
          } else {
            high <- high + 5
          }
        }
        h5(paste0("Showing ", low, " to ", high," of ", nrow(DB$cust_var), " variables"), style = "color: white; font-size: 10px;")
      }
    }
  })
  
  # Message on Database tabs if no scheme available yet
  observe({
    if(!is.null(DB$exist)) {
      if(DB$exist){
        
        # Message for tab Browse Entries
        output$no_scheme_entries <- renderUI({
          fluidRow(
            column(1),
            column(
              width = 4,
              align = "left",
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'No scheme available.')
                  )
                )
              ),
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'Download a scheme first and type assemblies in the section Allelic Typing.')
                  )
                )
              )
            )
          )
        })
        
        # Message for Tab Scheme Info
        output$no_scheme_info <- renderUI({
          fluidRow(
            column(1),
            column(
              width = 10,
              align = "left",
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'No scheme available.')
                  )
                )
              ),
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'Download a scheme first and type assemblies in the section Allelic Typing.')
                  )
                )
              )
            )
          )
        })
        
        # Message for Tab Distance Matrix
        output$no_scheme_distancematrix <- renderUI({
          fluidRow(
            column(1),
            column(
              width = 10,
              align = "left",
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'No scheme available.')
                  )
                )
              ),
              p(
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; ', 
                              'Download a scheme first and type assemblies in the section Allelic Typing.')
                  )
                )
              )
            )
          )
        })
        
      } else {
        output$no_scheme_entries <- NULL
        output$no_scheme_info <- NULL
        output$no_scheme_distancematrix <- NULL
      }
    }
    
  })
  
  observe({
    # Conditional Missing Values Tab
    if(!is.null(DB$allelic_profile)) {
      if(anyNA(DB$allelic_profile)) {
        if(isFALSE(DB$no_na_switch)) {
          output$menu_typing <- renderMenu(
            sidebarMenu(
              menuItem(
                text = "Database",
                tabName = "database",
                icon = icon("hard-drive"),
                startExpanded = TRUE,
                menuSubItem(
                  text = "Browse Entries",
                  tabName = "db_browse_entries"
                ),
                menuSubItem(
                  text = "Scheme Info",
                  tabName = "db_schemeinfo"
                ),
                menuSubItem(
                  text = "Loci Info",
                  tabName = "db_loci_info"
                ),
                menuSubItem(
                  text = "Distance Matrix",
                  tabName = "db_distmatrix"
                ),
                menuSubItem(
                  text = "Missing Values",
                  tabName = "db_missing_values",
                  selected = TRUE,
                  icon = icon("triangle-exclamation")
                )
              ),
              menuItem(
                text = "Schemes",
                tabName = "init",
                icon = icon("layer-group")
              ),
              menuItem(
                text = "Allelic Typing",
                tabName = "typing",
                icon = icon("gears")
              ),
              menuItem(
                text = "Visualization",
                tabName = "visualization",
                icon = icon("circle-nodes")
              )
            )
          )
          
          if(!is.null(DB$scheme)) {
            amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                             amrfinder_species = amrfinder_species)
            
            if(!isFALSE(amrfinder_available)) {
              
              output$menu_screening <- renderMenu(screening_menu_available)
              
            } else {
              output$menu_screening <- renderMenu(screening_menu_available)
            }
          }
        }
        
      } else {
        output$menu_typing <- renderMenu(
          sidebarMenu(
            menuItem(
              text = "Database",
              tabName = "database",
              icon = icon("hard-drive"),
              startExpanded = TRUE,
              menuSubItem(
                text = "Browse Entries",
                tabName = "db_browse_entries"
              ),
              menuSubItem(
                text = "Scheme Info",
                tabName = "db_schemeinfo"
              ),
              menuSubItem(
                text = "Loci Info",
                tabName = "db_loci_info"
              ),
              menuSubItem(
                text = "Distance Matrix",
                tabName = "db_distmatrix"
              )
            ),
            menuItem(
              text = "Schemes",
              tabName = "init",
              icon = icon("layer-group")
            ),
            menuItem(
              text = "Allelic Typing",
              tabName = "typing",
              icon = icon("gears")
            ),
            menuItem(
              text = "Visualization",
              tabName = "visualization",
              icon = icon("circle-nodes")
            )
          )
        )
        
        if(!is.null(DB$scheme)) {
          amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                           amrfinder_species = amrfinder_species)
          
          if(!isFALSE(amrfinder_available)) {
            
            output$menu_screening <- renderMenu(screening_menu_available)
            
          } else {
            output$menu_screening <- renderMenu(screening_menu_available)
          }
        }
      }
    }
    
  })
  
  observe({
    
    if (!is.null(DB$available)) {
      output$scheme_db <- renderUI({
        if (length(DB$available) > 3) {
          selectInput(
            "scheme_db",
            label = "",
            choices = if(!is.null(Typing$last_scheme)) {
              Typing$last_scheme
            } else {DB$available},
            selected = if(!is.null(Typing$last_scheme)) {
              Typing$last_scheme
            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
          )
        } else {
          prettyRadioButtons(
            "scheme_db",
            label = "",
            choices = if(!is.null(Typing$last_scheme)) {
              Typing$last_scheme
            } else {DB$available},
            selected = if(!is.null(Typing$last_scheme)) {
              Typing$last_scheme
            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
          )
        }
      })
      
      if (!is.null(DB$schemeinfo)) {
        
        output$scheme_info <- renderTable({
          DB$schemeinfo
        }, sanitize.text.function = function(x) x) 
        
      } else {
        
        output$scheme_info <- NULL
      }
      
      if (!is.null(DB$loci_info)) {
        req()
        loci_info <- DB$loci_info
        names(loci_info)[6] <- "Allele Count"
        
        output$db_loci <- renderDataTable(
          loci_info,
          selection = "single",
          options = list(pageLength = 15,  
                         autoWidth = TRUE,
                         lengthMenu = list(c(15), c('15')), 
                         columnDefs = list(list(searchable = TRUE,
                                                targets = "_all",
                                                className = "dt-left")),
                         initComplete = DT::JS(
                           "function(settings, json) {",
                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                           "}"
                         ),
                         drawCallback = DT::JS(
                           "function(settings) {",
                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                           "}"
                         ))
        )
        
        output$db_loci_no <- NULL
        output$loci_info_text <- renderUI(
          p(
            HTML(
              paste0(
                '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                'Information about loci included in the scheme and their respective alleles.',
                '</span>'
              )
            )
          )
        )
        
      } else {
        if(!is.null(DB$scheme_db) & !is.null(DB$scheme) & !is.null(DB$scheme_link)) {
          if(!is.null(DB$scheme_db) & !is.null(DB$scheme) & !is.null(DB$scheme_link)) {
            output$db_loci_no <- renderUI(
              p(
                HTML(
                  paste0(
                    '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
                    '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                    'Locus information not available for ',
                    DB$scheme, 
                    if(DB$scheme_db == "pubMLST") {
                      paste0('. Check database online: ',
                             ' <a href="', DB$scheme_link , '" target="_blank" style="color:#008edb; text-decoration:none;">', DB$scheme_db , '</a>.')
                    },
                    '</span>'
                  )
                )
              )
            )
            output$loci_info_text <- NULL
          }
        }
        output$db_loci <- NULL
      }
    } 
  })
  
  # If only one entry available disable varying loci checkbox
  
  output$compare_difference_box <- renderUI({
    if(!is.null(DB$data)) {
      if(nrow(DB$data) > 1) {
        div(
          class = "mat-switch-loci",
          materialSwitch(
            "compare_difference",
            h5(p("Only Varying Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
            value = FALSE,
            right = TRUE
          )
        )
      }
    }
  })
  
  ### Database Events ----
  
  # Shutdown
  observeEvent(input$shutdown, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'Are you sure you want to stop the application?',
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Close PhyloTrace",
          easyClose = TRUE,
          footer = tagList(
            modalButton("Dismiss"),
            actionButton("conf_shutdown", "Close", class = "load-db", width = "100px")
          )
        )
      )
    )
  })
  
  observeEvent(input$conf_shutdown, {
    shinyjs::runjs("window.close();")
    stopApp()
  })
  
  # Support menu
  observeEvent(input$support_menu, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'For help refer to the ',
                    '<a href="https://www.phylotrace.com/user-manual" target="_blank">User Manual</a>',
                    '.',
                    '</span>'
                  )
                )
              ),
              br(),
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px; display: block">',
                    'If issues persist or for any other inquiries contact us at <a href="mailto:info@phylotrace.com">info@phylotrace.com</a>.',
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Help",
          easyClose = TRUE,
          footer = tagList(
            modalButton("Dismiss")
          )
        )
      )
    )
  })
  
  # Settings menu
  observeEvent(input$settings_menu, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'Coming soon ... ',
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Settings",
          easyClose = TRUE,
          footer = tagList(
            modalButton("Dismiss")
          )
        )
      )
    )
  })
  
  # Show custom variable table on button input
  observeEvent(input$custom_var_table, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          column(
            width = 12,
            dataTableOutput("show_cust_var"),
            br(),
            br()
          ),
          title = "Custom Variables Overview",
          easyClose = TRUE,
          footer = tagList(
            actionButton("dismiss_cust_var_table", "Dismiss", class = "load-db", width = "100px")
          )
        )
      )
    )
  })
  
  observeEvent(input$dismiss_cust_var_table, {
    removeModal()
  })
  
  # Invalid entries table input
  observe({
    req(DB$data, input$db_entries)
    if (isTRUE(input$invalid_date)) {
      show_toast(
        title = "Invalid date",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
      DB$inhibit_change <- TRUE
    } else if(isTRUE(input$empty_name)) {
      show_toast(
        title = "Empty name",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
      DB$inhibit_change <- TRUE
    } else if(isTRUE(input$empty_id)) {
      show_toast(
        title = "Empty ID",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
      DB$inhibit_change <- TRUE
    } else {
      DB$inhibit_change <- FALSE
    }
  })
  
  # Change scheme
  observeEvent(input$reload_db, {
    
    log_print("Input reload_db")
    
    if(tail(readLines(file.path(logdir, "script_log.txt")), 1)!= "0") {
      show_toast(
        title = "Pending Multi Typing",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else if(Screening$status == "started") {
      show_toast(
        title = "Pending Screening",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      showModal(
        div(
          class = "start-modal",
          modalDialog(
            fluidRow(
              br(), 
              column(
                width = 11,
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                      'Select available scheme',
                      '</span>'
                    )
                  )
                ),
                div(
                  class = "modal-element",
                  selectInput(
                    "scheme_db",
                    label = "",
                    choices = DB$available,
                    selected = DB$scheme
                  )
                ),
                br()
              ),
              br()
            ),
            title = "Load Database",
            easyClose = TRUE,
            footer = tagList(
              modalButton("Dismiss"),
              actionButton("load", "Load", class = "load-db", width = "100px")
            )
          )
        )
      )
    }
  })
  
  # Create new database
  observe({
    shinyDirChoose(input,
                   "create_new_db",
                   roots = c(Home = path_home(), Root = "/"),
                   defaultRoot = "Home",
                   session = session)
    
    if(!is.null(input$create_new_db)) {
      DB$new_database <- as.character(
        parseDirPath(
          roots = c(Home = path_home(), Root = "/"),
          input$create_new_db
        )
      )
    }
  })
  
  # Undo db changes
  observeEvent(input$undo_changes, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input undo_changes")
    
    DB$inhibit_change <- FALSE
    
    Data <- readRDS(paste0(
      Startup$database, "/",
      gsub(" ", "_", DB$scheme),
      "/Typing.rds"
    ))
    
    DB$data <- Data[["Typing"]]
    
    if ((ncol(DB$data)-13) != DB$number_loci) {
      cust_var <- select(DB$data, 14:(ncol(DB$data) - DB$number_loci))
      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
    } else {
      DB$cust_var <- data.frame()
    }
    
    DB$change <- FALSE
    DB$count <- 0
    DB$no_na_switch <- TRUE
    DB$meta_gs <- select(DB$data, c(1, 3:13))
    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
    DB$deleted_entries <- character(0)
    
    observe({
      req(DB$data)
      
      if(nrow(DB$data) == 1) {
        if(!is.null(DB$data) & !is.null(DB$cust_var)) {
          output$db_entries <- renderRHandsontable({
            rhandsontable(
              select(DB$data, 1:(13 + nrow(DB$cust_var))),
              error_highlight = err_thresh() - 1,                              
              rowHeaders = NULL,
              contextMenu = FALSE,
              highlightCol = TRUE, 
              highlightRow = TRUE
            ) %>%
              hot_col(1, 
                      valign = "htMiddle",
                      halign = "htCenter") %>%
              hot_col(3, readOnly = TRUE) %>%
              hot_col(c(1, 5, 10, 11, 12, 13),
                      readOnly = TRUE) %>%
              hot_col(3:(13 + nrow(DB$cust_var)), 
                      valign = "htMiddle",
                      halign = "htLeft") %>%
              hot_col(3, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
              hot_col(4, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
              hot_col(8, type = "dropdown", source = country_names) %>%
              hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                      validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }") %>%
              hot_cols(fixedColumnsLeft = 1) %>%
              hot_col(2, type = "checkbox", width = "auto",
                      valign = "htTop",
                      halign = "htCenter") %>%
              hot_rows(fixedRowsTop = 0) %>%
              hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.error_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
                                                             }
                                                           }
                                                       }") 
          })
        }
      } else if (between(nrow(DB$data), 1, 40)) {
        if (length(input$compare_select) > 0) {
          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
            output$db_entries <- renderRHandsontable({
              
              if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                entry_data <- DB$data %>%
                  select(1:(13 + nrow(DB$cust_var))) %>%
                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
                
                rhandsontable(
                  entry_data,
                  col_highlight = diff_allele() - 1,
                  dup_names_high = duplicated_names() - 1,
                  dup_ids_high = duplicated_ids() - 1,
                  row_highlight = true_rows() - 1,
                  error_highlight = err_thresh() - 1,
                  rowHeaders = NULL,
                  highlightCol = TRUE, 
                  highlightRow = TRUE,
                  contextMenu = FALSE,
                  height = entry_table_height()
                )  %>%
                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                          valign = "htMiddle",
                          halign = "htCenter",
                          readOnly = TRUE) %>%
                  hot_col(1, 
                          valign = "htMiddle",
                          halign = "htCenter") %>%
                  hot_col(3, readOnly = TRUE) %>%
                  hot_col(c(1, 5, 10, 11, 12, 13),
                          readOnly = TRUE) %>%
                  hot_col(3:(13 + nrow(DB$cust_var)), 
                          valign = "htMiddle",
                          halign = "htLeft") %>%
                  hot_col(3, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(4, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(8, type = "dropdown", source = country_names) %>%
                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                          validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }") %>%
                  hot_col(2, type = "checkbox", width = "auto",
                          valign = "htTop",
                          halign = "htCenter",
                          strict = TRUE,
                          allowInvalid = FALSE,
                          copyable = TRUE) %>%
                  hot_cols(fixedColumnsLeft = 1) %>%
                  hot_rows(fixedRowsTop = 0) %>%
                  hot_col(1, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.row_highlight
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                         }
  
                       }
              }") %>%
                  hot_col(diff_allele(),
                          renderer = "
                  function(instance, td, row, col, prop, value, cellProperties) {
                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
  
                    if (instance.params) {
                          hcols = instance.params.col_highlight;
                          hcols = hcols instanceof Array ? hcols : [hcols];
                        }
  
                    if (instance.params && hcols.includes(col)) {
                      td.style.background = 'rgb(116, 188, 139)';
                    }
                }"
                  ) %>%
                  hot_col(4, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_names_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(3, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_ids_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.error_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                             }
                                                           }
                                                       }")  
              }
            })
          }
        } else {
          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
            output$db_entries <- renderRHandsontable({
              
              if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                rhandsontable(
                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
                  rowHeaders = NULL,
                  row_highlight = true_rows() - 1,
                  dup_names_high = duplicated_names()- 1,
                  dup_ids_high = duplicated_ids() - 1,
                  error_highlight = err_thresh() - 1,
                  contextMenu = FALSE,
                  highlightCol = TRUE, 
                  highlightRow = TRUE,
                  height = entry_table_height()
                ) %>%
                  hot_cols(fixedColumnsLeft = 1) %>%
                  hot_col(1, 
                          valign = "htMiddle",
                          halign = "htCenter") %>%
                  hot_col(3, readOnly = TRUE) %>%
                  hot_col(c(1, 5, 10, 11, 12, 13),
                          readOnly = TRUE) %>%
                  hot_col(3:(13 + nrow(DB$cust_var)), 
                          valign = "htMiddle",
                          halign = "htLeft") %>%
                  hot_col(3, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(4, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(8, type = "dropdown", source = country_names) %>%
                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                          validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }") %>%
                  hot_col(2, type = "checkbox", width = "auto",
                          valign = "htTop",
                          halign = "htCenter") %>%
                  hot_rows(fixedRowsTop = 0) %>%
                  hot_col(1, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.row_highlight
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                         }
  
                       }
              }") %>%
                  hot_col(4, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_names_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(3, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_ids_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.error_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                             }
                                                           }
                                                       }")  
              }
            })    
          }
        }
      } else {
        if (length(input$compare_select) > 0) {
          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
            
            output$db_entries <- renderRHandsontable({
              
              if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                w$show()
                
                entry_data <- DB$data %>%
                  select(1:(13 + nrow(DB$cust_var))) %>%
                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
                
                tab <- rhandsontable(
                  entry_data,
                  col_highlight = diff_allele() - 1,
                  rowHeaders = NULL,
                  height = entry_table_height(),
                  row_highlight = true_rows() - 1,
                  dup_names_high = duplicated_names() - 1,
                  dup_ids_high = duplicated_ids() - 1,
                  error_highlight = err_thresh() - 1,
                  contextMenu = FALSE,
                  highlightCol = TRUE, 
                  highlightRow = TRUE
                ) %>%
                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                          readOnly = TRUE, 
                          valign = "htMiddle",
                          halign = "htCenter") %>%
                  hot_col(3:(13 + nrow(DB$cust_var)), 
                          valign = "htMiddle",
                          halign = "htLeft") %>%
                  hot_col(3, readOnly = TRUE) %>%
                  hot_col(3, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(4, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(c(1, 5, 10, 11, 12, 13),
                          readOnly = TRUE) %>%
                  hot_col(8, type = "dropdown", source = country_names) %>%
                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                          validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }") %>%
                  hot_col(1, 
                          valign = "htMiddle",
                          halign = "htCenter") %>%
                  hot_col(2, type = "checkbox", width = "auto",
                          valign = "htTop",
                          halign = "htCenter",
                          allowInvalid = FALSE,
                          copyable = TRUE) %>%
                  hot_cols(fixedColumnsLeft = 1) %>%
                  hot_rows(fixedRowsTop = 0) %>%
                  hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.row_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                                                             }
                                                           }
                                                       }") %>%
                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.error_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                             }
                                                           }
                                                       }") %>%
                  hot_col(4, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_names_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(3, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_ids_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(diff_allele(),
                          renderer = "
                  function(instance, td, row, col, prop, value, cellProperties) {
                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
  
                    if (instance.params) {
                          hcols = instance.params.col_highlight;
                          hcols = hcols instanceof Array ? hcols : [hcols];
                        }
  
                    if (instance.params && hcols.includes(col)) {
                      td.style.background = 'rgb(116, 188, 139)';
                    }
                }") 
                
                shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                return(tab) 
              }
            })
          }
        } else {
          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
            output$db_entries <- renderRHandsontable({
              if(!any(input$compare_select %in% colnames(DB$allelic_profile) != TRUE)) {
                shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
                w$show()
                
                tab <- rhandsontable(
                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
                  rowHeaders = NULL,
                  height = entry_table_height(),
                  dup_names_high = duplicated_names() - 1,
                  dup_ids_high = duplicated_ids() - 1,
                  row_highlight = true_rows() - 1,
                  error_highlight = err_thresh() - 1,
                  contextMenu = FALSE,
                  highlightCol = TRUE, 
                  highlightRow = TRUE
                ) %>%
                  hot_cols(fixedColumnsLeft = 1) %>%
                  hot_col(1, 
                          valign = "htMiddle",
                          halign = "htCenter") %>%
                  hot_col(c(1, 5, 10, 11, 12, 13),
                          readOnly = TRUE) %>%
                  hot_col(3, readOnly = TRUE) %>%
                  hot_col(3, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(4, validator = "
                                  function(value, callback) {
                                    try {
                                      if (value === null || value.trim() === '') {
                                        callback(false); // Cell is empty
                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                      } else {
                                        callback(true); // Cell is not empty
                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
                                      }
                                    } catch (err) {
                                      console.log(err);
                                      callback(false); // In case of error, consider it as invalid
                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
                                    }
                                  }
                                ") %>%
                  hot_col(8, type = "dropdown", source = country_names) %>%
                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                          validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }") %>%
                  hot_col(3:(13 + nrow(DB$cust_var)), 
                          valign = "htMiddle",
                          halign = "htLeft") %>%
                  hot_rows(fixedRowsTop = 0) %>%
                  hot_col(1, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.row_highlight
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
                         }
                       }
              }") %>%
                  hot_col(2, type = "checkbox", width = "auto",
                          valign = "htTop", halign = "htCenter") %>%
                  hot_col(4, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_names_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(3, renderer = "
              function (instance, td, row, col, prop, value, cellProperties) {
                       Handsontable.renderers.TextRenderer.apply(this, arguments);
  
                       if (instance.params) {
                         hrows = instance.params.dup_ids_high
                         hrows = hrows instanceof Array ? hrows : [hrows]
  
                         if (hrows.includes(row)) { 
                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
                         }
                       }
              }") %>%
                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
                                                           if (instance.params) {
                                                             hrows = instance.params.error_highlight
                                                             hrows = hrows instanceof Array ? hrows : [hrows]
                                                             if (hrows.includes(row)) { 
                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
                                                             }
                                                           }
                                                       }") 
                
                shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
                return(tab) 
              }
            })
          }
        }
      }
    })
  })
  
  observe({
    if(!is.null(DB$data)){
      if ((ncol(DB$data)-13) != DB$number_loci) {
        cust_var <- select(DB$data, 14:(ncol(DB$data) - DB$number_loci))
        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
      } else {
        DB$cust_var <- data.frame()
      }
    }
  })
  
  DB$count <- 0
  
  observeEvent(input$add_new_variable, {
    log_print("Input add_new_variable")
    
    if(nchar(input$new_var_name) > 12) {
      log_print("Add variable; max. 10 character")
      show_toast(
        title = "Max. 10 characters",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      if (input$new_var_name == "") {
        log_print("Add variable; min. 1 character")
        show_toast(
          title = "Min. 1 character",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
      } else {
        if(trimws(input$new_var_name) %in% names(DB$meta)) {
          log_print("Add variable; name already existing")
          show_toast(
            title = "Variable name already existing",
            type = "warning",
            position = "bottom-end",
            timer = 6000
          )
        } else {
          showModal(
            div(
              class = "start-modal",
              modalDialog(
                fluidRow(
                  br(), 
                  column(
                    width = 11,
                    p(
                      HTML(
                        paste0(
                          '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                          'Choose variable type',
                          '</span>'
                        )
                      )
                    ),
                    div(
                      class = "modal-element",
                      selectInput(
                        "new_var_type",
                        label = "",
                        choices = c("Categorical (character)",
                                    "Continous (numeric)")
                      )
                    )
                  ),
                  br()
                ),
                title = "Select Data Type",
                easyClose = TRUE,
                footer = tagList(
                  modalButton("Cancel"),
                  actionButton("conf_new_var", "Confirm", class = "btn btn-default")
                )
              )
            )
          )
        }
      }
    }
  })
  
  observeEvent(input$conf_new_var, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input conf_new_var")
    
    # User feedback variables
    removeModal()
    DB$count <- DB$count + 1
    DB$change <- TRUE
    
    # Format variable name
    name <- trimws(input$new_var_name)
    
    if(input$new_var_type == "Categorical (character)") {
      DB$data <- DB$data %>%
        mutate("{name}" := character(nrow(DB$data)), .after = 13)
      
      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
    } else {
      DB$data <- DB$data %>%
        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
      
      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
    }
    
    DB$meta_gs <- select(DB$data, c(1, 3:13))
    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
    
    log_print(paste0("New custom variable added: ", input$new_var_name))
    
    show_toast(
      title = paste0("Variable ", trimws(input$new_var_name), " added"),
      type = "success",
      position = "bottom-end",
      timer = 6000
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')  
  })
  
  observeEvent(input$delete_new_variable, {
    log_print("Input delete_new_variable")
    
    if (input$del_which_var == "") {
      log_print("Delete custom variables; no custom variable")
      show_toast(
        title = "No custom variables",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      showModal(
        div(
          class = "start-modal",
          modalDialog(
            fluidRow(
              br(), 
              column(
                width = 11,
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                      "Confirmation will lead to irreversible deletion of the custom ",
                      input$del_which_var,
                      " variable. Continue?",
                      '</span>'
                    )
                  )
                )
              ),
              br()
            ),
            title = "Delete custom variables",
            fade = TRUE,
            easyClose = TRUE,
            footer = tagList(
              modalButton("Cancel"),
              actionButton("conf_var_del", "Delete", class = "btn btn-danger")
            )
          )
        )
      )
    }
  })
  
  observeEvent(input$conf_var_del, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input conf_var_del")
    
    DB$change <- TRUE
    
    removeModal()
    
    if(DB$count >= 1) {
      DB$count <- DB$count - 1
    } 
    
    show_toast(
      title = paste0("Variable ", input$del_which_var, " removed"),
      type = "warning",
      position = "bottom-end",
      timer = 6000
    )
    
    log_print(paste0("Variable ", input$del_which_var, " removed"))
    
    DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
    DB$data <- select(DB$data, -(input$del_which_var))
    DB$meta_gs <- select(DB$data, c(1, 3:13))
    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
    
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Select all button
  
  observeEvent(input$sel_all_entries, {
    log_print("Input sel_all_entries")
    
    DB$data$Include <- TRUE
  })
  
  observeEvent(input$desel_all_entries, {
    log_print("Input desel_all_entries")
    
    DB$data$Include <- FALSE
  })
  
  # Switch to entry table
  
  observeEvent(input$change_entries, {
    log_print("Input change_entries")
    
    removeModal()
    updateTabItems(session, "tabs", selected = "db_browse_entries")
  })
  
  #### Save Missing Value as CSV ----
  
  output$download_na_matrix <- downloadHandler(
    filename = function() {
      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
    },
    content = function(file) {
      download_matrix <- hot_to_r(input$table_missing_values)
      write.csv(download_matrix, file, sep = ",", row.names=FALSE, quote=FALSE) 
    }
  )
  
  #### Save scheme info table as CSV ----
  
  output$download_schemeinfo <- downloadHandler(
    filename = function() {
      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
      
      paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
    },
    content = function(file) {
      if(any(DB$schemeinfo[,1] == "Publications")) {
        pub_index <- which(DB$schemeinfo[,1] == "Publications")
        write.table(
          DB$schemeinfo[1:(pub_index-1),],
          file, 
          sep = ";",
          row.names = FALSE, 
          quote = FALSE
        )
      } else {
        write.table(
          DB$schemeinfo,
          file, 
          sep = ";",
          row.names = FALSE, 
          quote = FALSE
        )
      }
    }
  )
  
  #### Save Loci info table as CSV ----
  
  output$download_loci_info <- downloadHandler(
    filename = function() {
      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
      
      paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
    },
    content = function(file) {
      write.table(
        DB$loci_info,
        file, 
        sep = ";",
        row.names = FALSE, 
        quote = FALSE
      ) 
    }
  )
  
  #### Save entry table as CSV ----
  
  output$download_entry_table <- downloadHandler(
    filename = function() {
      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
      
      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
    },
    content = function(file) {
      download_matrix <- hot_to_r(input$db_entries)
      
      if(isFALSE(input$download_table_hashes)) {
        included_loci <- colnames(select(download_matrix, -(1:(13 + nrow(DB$cust_var)))))
        full_hashes <- DB$allelic_profile[included_loci]
        download_matrix[included_loci] <- full_hashes
      }
      
      if(isTRUE(input$download_table_include)) {
        download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
      }
      
      if(isFALSE(input$download_table_loci)) {
        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
      } 
      
      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
    }
  )
  
  # Save Edits Button
  
  observeEvent(input$edit_button, {
    if(nrow(hot_to_r(input$db_entries)) > nrow(DB$data)) {
      show_toast(
        title = "Invalid rows entered. Saving not possible.",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      if(!isTRUE(DB$inhibit_change)) {
        log_print("Input edit_button")
        
        showModal(
          div(
            class = "start-modal",
            modalDialog(
              if(length(DB$deleted_entries > 0)) {
                fluidRow(
                  br(), 
                  column(
                    width = 11,
                    p(
                      HTML(
                        paste0(
                          '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                          "Overwriting previous metadata of local ",
                          DB$scheme,
                          " database. Deleted entries will be irreversibly removed. Continue?",
                          '</span>'
                        )
                      )
                    )
                  ),
                  br()
                )
              } else {
                fluidRow(
                  br(), 
                  column(
                    width = 11,
                    p(
                      HTML(
                        paste0(
                          '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                          "Overwriting previous metadata of local ",
                          DB$scheme,
                          " database. Continue?",
                          '</span>'
                        )
                      )
                    )
                  ),
                  br()
                )
              },
              title = "Save Database",
              fade = TRUE,
              easyClose = TRUE,
              footer = tagList(
                modalButton("Cancel"),
                actionButton("conf_db_save", "Save", class = "btn btn-default")
              )
            )
          )
        )
      } else {
        log_print("Input edit_button, invalid values.")
        show_toast(
          title = "Invalid values entered. Saving not possible.",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
      }
    }
  })
  
  observeEvent(input$Cancel, {
    log_print("Input Cancel")
    removeModal()
  })
  
  observeEvent(input$conf_db_save, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    log_print("Input conf_db_save")
    
    # Remove isolate assembly file if present
    if(!is.null(DB$remove_iso)) {
      if(length(DB$remove_iso) > 0) {
        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
      }
    }
    DB$remove_iso <- NULL
    
    Data <- readRDS(file.path(Startup$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
    
    if ((ncol(Data[["Typing"]]) - 13) != DB$number_loci) {
      cust_vars_pre <- select(Data[["Typing"]], 
                              14:(ncol(Data[["Typing"]]) - DB$number_loci))
      cust_vars_pre <- names(cust_vars_pre)
    } else {
      cust_vars_pre <- character()
    }
    
    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
    
    meta_hot <- hot_to_r(input$db_entries) %>%
      select(1:(13 + nrow(DB$cust_var))) 
    
    if(length(DB$deleted_entries > 0)) {
      
      meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
      
      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
                                 meta_hot, .before = 1)
      rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
    } else {
      Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
    }
    
    # Ensure correct logical data type
    Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
    saveRDS(Data, file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
    
    # Load database from files  
    Database <- readRDS(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
    
    DB$data <- Database[["Typing"]]
    
    if(!is.null(DB$data)){
      if ((ncol(DB$data)-13) != DB$number_loci) {
        cust_var <- select(DB$data, 14:(ncol(DB$data) - DB$number_loci))
        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
      } else {
        DB$cust_var <- data.frame()
      }
    }
    
    DB$change <- FALSE
    DB$count <- 0
    DB$no_na_switch <- TRUE
    DB$meta_gs <- select(DB$data, c(1, 3:13))
    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
    DB$deleted_entries <- character(0)
    
    removeModal()
    
    show_toast(
      title = "Database successfully saved",
      type = "success",
      position = "bottom-end",
      timer = 4000
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  observeEvent(input$del_button, {
    log_print("Input del_button")
    
    if (length(input$select_delete) < 1) {
      log_print("Delete entries; no entry selected")
      show_toast(
        title = "No entry selected",
        type = "warning",
        position = "bottom-end",
        timer = 4000
      )
    } else {
      if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
        showModal(
          div(
            class = "start-modal",
            modalDialog(
              fluidRow(
                br(), 
                column(
                  width = 11,
                  p(
                    HTML(
                      paste0(
                        '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                        "Deleting will lead to removal of <strong>ALL entries</strong> and assemblies from local ", 
                        DB$scheme, 
                        " database. The data can not be recovered afterwards. Continue?",
                        '</span>'
                      )
                    )
                  )
                ),
                br()
              ),
              easyClose = TRUE,
              title = "Deleting Entries",
              footer = tagList(
                modalButton("Cancel"),
                actionButton("conf_delete_all", "Delete")
              )
            )
          )
        )
      } else {
        showModal(
          div(
            class = "start-modal",
            modalDialog(
              fluidRow(
                br(), 
                column(
                  width = 11,
                  p(
                    HTML(
                      paste0(
                        '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                        "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?",
                        '</span>'
                      )
                    )
                  )
                ),
                br()
              ),
              title = "Deleting Entries",
              fade = TRUE,
              easyClose = TRUE,
              footer = tagList(
                modalButton("Cancel"),
                actionButton(
                  "conf_delete", 
                  "Delete"
                )
              )
            )
          )
        )
      }
    }
  })
  
  observeEvent(input$conf_delete_all, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input conf_delete_all")
    
    # remove file with typing data
    file.remove(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
    unlink(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
    
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'All entries have been removed. Select a local database to load.',
                    '</span>'
                  )
                )
              ),
              div(
                class = "modal-element",
                selectInput(
                  "scheme_db",
                  label = "",
                  choices = if(!is.null(Typing$last_scheme)) {
                    Typing$last_scheme
                  } else {DB$available},
                  selected = if(!is.null(Typing$last_scheme)) {
                    Typing$last_scheme
                  } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
                )
              )
            ),
            br()
          ),
          title = "Load Database",
          footer = tagList(
            actionButton("load", "Load", class = "load-db", width = "100px")
          )
        )
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  DB$deleted_entries <- character(0)
  
  observeEvent(input$conf_delete, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input conf_delete")
    
    # Get isolates selected for deletion
    DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
    
    # Set reactive status variables
    DB$no_na_switch <- TRUE
    DB$change <- TRUE
    DB$check_new_entries <- FALSE
    
    # Set isolate directory deletion variables
    isopath <- dir_ls(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Isolates"))
    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
    
    # Reload updated database reactive variables
    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
    DB$meta_gs <- select(DB$data, c(1, 3:13))
    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
    
    # User feedback
    removeModal()
    
    if(length(input$select_delete) > 1) {
      show_toast(
        title = "Entries deleted",
        type = "success",
        position = "bottom-end",
        timer = 4000
      )
    } else {
      show_toast(
        title = "Entry deleted",
        type = "success",
        position = "bottom-end",
        timer = 4000
      )
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ### Distance Matrix ---- 
  
  hamming_df <- reactive({
    req(DB$data, DB$allelic_profile)
    
    if(isTRUE(input$distmatrix_true)) {
      if(isTRUE(any(DB$data$Include == TRUE))) {
        if(anyNA(DB$allelic_profile)) {
          if(input$na_handling == "omit") {
            allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
            
            allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
            
            hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
            
          } else if(input$na_handling == "ignore_na"){
            hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
            
          } else {
            hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
            
          } 
        } else {
          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
        }
      } else {
        show_toast(
          title = "No isolates selected",
          type = "warning",
          position = "bottom-end",
          timer = 2000
        )
        return(NULL)
      }
    } else {
      if(anyNA(DB$allelic_profile)) {
        if(input$na_handling == "omit") {
          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
        } else if(input$na_handling == "ignore_na"){
          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
        } else {
          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
        }  
      } else {
        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
      }
      
      
      # Extreme values for distance matrix heatmap display
      DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
      DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
      
      if(isFALSE(input$distmatrix_triangle)) {
        hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
      } 
      
      # Row- and colnames change
      if(isTRUE(input$distmatrix_true)) {
        rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
      } else {
        rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
      }
      colnames(hamming_mat) <- rownames(hamming_mat)
      
      mode(hamming_mat) <- "integer"
      
      DB$ham_matrix <- hamming_mat %>%
        as.data.frame() %>%
        mutate(Index = colnames(hamming_mat)) %>%
        relocate(Index)
      
      return(DB$ham_matrix)
    }
  })
  
  output$download_distmatrix <- downloadHandler(
    filename = function() {
      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Distance_Matrix.csv")
    },
    content = function(file) {
      download_matrix <- hot_to_r(input$db_distancematrix)
      download_matrix[is.na(download_matrix)] <- ""
      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
    }
  )
  
  # _______________________ ####
  
  ## Locus sequences ----
  
  observe({
    if(!is.null(Startup$database) & !is.null(DB$scheme)) {
      DB$loci <- list.files(
        path = paste0(Startup$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
        pattern = "\\.(fasta|fa|fna)$",
        full.names = TRUE
      )
    }
  })
  
  observe({
    req(DB$data)
    if (!is.null(DB$loci_info)) {
      loci_info <- DB$loci_info
      names(loci_info)[6] <- "Allele Count"
      
      output$db_loci <- renderDataTable(
        loci_info,
        selection = "single",
        options = list(pageLength = 15,  
                       lengthMenu = list(c(15), c('15')), 
                       columnDefs = list(list(searchable = TRUE,
                                              targets = "_all")),
                       initComplete = DT::JS(
                         "function(settings, json) {",
                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                         "}"
                       ),
                       drawCallback = DT::JS(
                         "function(settings) {",
                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                         "}"
                       ))
      )
      
      output$db_loci_no <- NULL
      output$loci_info_text <- renderUI(
        p(
          HTML(
            paste0(
              '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
              'Information about loci included in the scheme and their respective alleles.',
              '</span>'
            )
          )
        )
      )
    } else {
      if(!is.null(DB$scheme_db) & !is.null(DB$scheme) & !is.null(DB$scheme_link)) {
        output$db_loci_no <- renderUI(
          p(
            HTML(
              paste0(
                '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
                '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
                'Locus information not available for ',
                DB$scheme, '. Check database online: ',
                ' <a href="', DB$scheme_link , '" target="_blank" style="color:#008edb; text-decoration:none;">', DB$scheme_db , '</a>.',
                '</span>'
              )
            )
          )
        )
        
        output$loci_info_text <- NULL
      }
      output$db_loci <- NULL
    }
  })
  
  output$loci_sequences <- renderUI({
    if (!is.null(DB$loci_info)) {
      req(input$db_loci_rows_selected, Startup$database, DB$scheme, input$seq_sel)
      
      DB$loci <- list.files(
        path = paste0(Startup$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
        pattern = "\\.(fasta|fa|fna)$",
        full.names = TRUE
      )
      
      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
      select <- which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1
      
      if(length(select) > 0) {
        seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
        
        DB$seq <- seq
        
        div(
          class = "loci-sequence-column",
          column(
            width = 12,
            br(), br(),
            HTML(
              paste(
                tags$span(style='color: white; font-size: 13px; position:relative; left: 3px', 
                          sub(" -.*", "", input$seq_sel))
              )
            ),
            tags$pre(HTML(color_sequence(seq)), class = "sequence")
          )
        )
      } else {NULL}
    } else {NULL}
  })
  
  output$sequence_selector <- renderUI({
    if(!is.null(input$db_loci_rows_selected) & !is.null(DB$loci_info)) {
      
      req(input$db_loci_rows_selected, Startup$database, DB$scheme)
      
      DB$loci <- list.files(
        path = paste0(Startup$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
        pattern = "\\.(fasta|fa|fna)$",
        full.names = TRUE
      )
      
      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
      
      seq_names <- c()
      for (i in seq_along(fasta)) {
        if (startsWith(fasta[[i]], ">")) {
          name <- sub(">", "", fasta[[i]])
          seq_names <- c(seq_names, name)
        }
      }
      
      var_count <- table(DB$allelic_profile[gsub(".fasta", "", (basename(DB$loci[input$db_loci_rows_selected])))])
      
      vec <- prop.table(var_count)
      
      perc <- sapply(unname(vec), scales::percent, accuracy = 0.1)
      
      names(perc) <- names(vec)
      
      choices <- seq_names
      
      present <- which(choices %in% names(vec))
      absent <- which(!(choices %in% names(vec)))
      
      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
      
      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
      
      choices <- c(choices[present], choices[absent])
      
      names(choices) <- sapply(choices, function(x) {
        x <- strsplit(x, " ")[[1]]
        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
        paste(x, collapse = " ")
      })
      
      box(
        solidHeader = TRUE,
        status = "primary",
        width = "100%",
        title = "Select Allele",
        column(
          width = 12,
          br(),
          fluidRow(
            column(1),
            column(
              width = 10,
              align = "left",
              selectInput(
                "seq_sel",
                "",
                choices = choices,
                width = "85%"
              )
            )
          ),
          br(), br(),
          fluidRow(
            column(1),
            column(
              width = 3,
              align = "left",
              actionButton("copy_seq", "Sequence",
                           icon = icon("copy")),
              bsTooltip("copy_seq", "Copy the allele sequence <br> to clipboard", placement = "bottom", trigger = "hover")
            ),
            column(
              width = 3,
              align = "left",
              actionButton("copy_hash", "Hash",
                           icon = icon("copy")),
              bsTooltip("copy_hash", "Copy the allele<br>hash to clipboard", placement = "bottom", trigger = "hover")
            ),
            column(
              width = 3,
              align = "left",
              downloadBttn(
                "get_locus",
                style = "simple",
                label = "Locus",
                size = "sm",
                icon = icon("download")
              ),
              bsTooltip("get_locus_bttn", "Save locus file as FASTA", placement = "bottom", trigger = "hover")
            )
          ),
          br()
        )
      )
    }
  })
  
  observeEvent(input$copy_seq, {
    if(!is.null(DB$seq)) {
      session$sendCustomMessage("txt", DB$seq)
    }
    show_toast(
      title = "Copied sequence",
      type = "success",
      position = "bottom-end",
      timer = 2000
    )
  })
  
  observeEvent(input$copy_hash, {
    if(!is.null(input$seq_sel)) {
      session$sendCustomMessage("txt", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))
    }
    show_toast(
      title = "Copied hash",
      type = "success",
      position = "bottom-end",
      timer = 2000
    )
  })
  
  output$get_locus <- downloadHandler(
    filename = function() {
      fname <- basename(DB$loci[input$db_loci_rows_selected])
      log_print(paste0("Get locus fasta ", fname))
      fname
    },
    content = function(file) {
      cont <- readLines(DB$loci[input$db_loci_rows_selected])
      writeLines(cont, file)
    }
  )
  
  # _______________________ ####
  
  ## Download cgMLST ----
  
  ### Manage Schemes UI Elements ----
  
  observe({
    req(input$select_cgmlst)
    if(grepl("_PM", input$select_cgmlst)) {
      Scheme$link_scheme <- schemes$url[schemes$species == input$select_cgmlst]
      Scheme$link_cgmlst <- schemes$url[schemes$species == input$select_cgmlst]
      Scheme$link_targets <- NA
      Scheme$folder_name <- schemes$species[schemes$species == input$select_cgmlst]
    } else if(grepl("_CM", input$select_cgmlst)) {
      Scheme$link_scheme <- paste0(schemes$url[schemes$species == input$select_cgmlst], "/")
      Scheme$link_cgmlst <- paste0(schemes$url[schemes$species == input$select_cgmlst], "/alleles/")
      Scheme$link_targets <- paste0(schemes$url[schemes$species == input$select_cgmlst], "/locus/?content-type=csv")
      Scheme$folder_name <- schemes$species[schemes$species == input$select_cgmlst]
    }
  })
  
  observeEvent(input$download_cgMLST, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
    
    show_toast(
      title = paste("Download of", input$select_cgmlst,  "started"),
      type = "success",
      position = "bottom-start",
      timer = 5000
    )
    
    shinyjs::hide("download_cgMLST")
    shinyjs::show("downloading")
    
    # Disable pickerInput
    shinyjs::runjs("$('#select_cgmlst').prop('disabled', true);")
    shinyjs::runjs("$('#select_cgmlst').selectpicker('refresh');")
    
    if(length(DB$available) == 0) {
      saveRDS(DB$new_database, file.path(app_local_share_path, "new_db.rds"))
      dir.create(file.path(readRDS(file.path(app_local_share_path, "new_db.rds")), "Database"), recursive = TRUE)
    }
    
    DB$load_selected <- TRUE
    
    # Check if .downloaded_schemes folder exists and if not create it
    if (!dir.exists(file.path(Startup$database, ".downloaded_schemes"))) {
      dir.create(file.path(Startup$database, ".downloaded_schemes"), recursive = TRUE)
    }
    
    # Check if remains of old temporary folder exists and remove them
    if (dir.exists(file.path(Startup$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
      unlink(file.path(Startup$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
    }
    
    ### Download Loci Fasta Files
    
    options(timeout = 600)
    
    # Create a Progress object
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    
    progress$set(message = "Download Scheme", value = 0)
    
    tryCatch({
      if(grepl("_PM", input$select_cgmlst)) {
        download.alleles.PM(url_link = schemes$url[schemes$species == input$select_cgmlst],
                            database = Startup$database,
                            folder_name = Scheme$folder_name,
                            progress = progress)
        "Download successful!"
      } else if(grepl("_CM", input$select_cgmlst)) {
        download.alleles.CM(url_link = schemes$url[schemes$species == input$select_cgmlst],
                            database = Startup$database,
                            folder_name = Scheme$folder_name,
                            progress = progress)
        "Download successful!"
      }
    }, error = function(e) {
      paste("Error: ", e$message)
    })
    
    # Unzip the scheme in temporary folder
    unzip(
      zipfile = file.path(Startup$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
      exdir = file.path(Startup$database, 
                        Scheme$folder_name, 
                        paste0(Scheme$folder_name, ".tmp")
      )
    )
    
    # Download species info & image
    if(!is.null(Scheme$species_data)) {
      if(length(Scheme$species_data) > 0) {
        saveRDS(Scheme$species_data,
                file.path(Startup$database, 
                          schemes$species[schemes$species == input$select_cgmlst], 
                          paste0(schemes$species[schemes$species == input$select_cgmlst], ".rds")))
        
        if(length(Scheme$species_data) > 1) {
          for(i in seq_along(Scheme$species_data)) {
            # Download image
            destination_file <- file.path(Startup$database, 
                                          input$select_cgmlst, 
                                          paste0(gsub(" ", "_", Scheme$species_data[[i]]$Name$name), ".jpg"))
            response_download <- httr::GET(Scheme$species_data[[i]]$Image)
            
            if (response_download$status_code == 200) {
              writeBin(httr::content(response_download, "raw"), destination_file)
              response_download <- NULL
              log_print("Image downloaded successfully!")
            } else {
              log_print("Failed to download image.")
            }
          }
        } else {
          destination_file <- file.path(Startup$database, input$select_cgmlst,
                                        paste0(gsub(" ", "_", Scheme$species_data[[1]]$Name$name), ".jpg"))
          
          response_download <- httr::GET(Scheme$species_data[[1]]$Image)
          
          if (response_download$status_code == 200) {
            writeBin(httr::content(response_download, "raw"), destination_file)
            log_print("Image downloaded successfully!")
          } else {
            log_print("Failed to download image.")
          }
        }
      } else {log_print("Failed to download species data from NCBI.")} 
    } else {log_print("Failed to download species data from NCBI.")}
    
    log_print("Hashing downloaded database")
    shinyjs::show("hashing")
    shinyjs::hide("downloading")
    
    show_toast(
      title = paste("Hashing of", input$select_cgmlst,  "started"),
      type = "success",
      position = "bottom-start",
      timer = 5000
    )
    
    # Hash temporary folder
    hash_database(file.path(Startup$database, 
                            Scheme$folder_name, 
                            paste0(Scheme$folder_name, ".tmp")),
                  progress = progress)
    
    # Get list from local database
    local_db_filelist <- list.files(file.path(Startup$database, 
                                              Scheme$folder_name, 
                                              paste0(Scheme$folder_name, "_alleles")))
    
    if (!is_empty(local_db_filelist)) {
      # Get list from temporary database
      tmp_db_filelist <- list.files(file.path(Startup$database,
                                              Scheme$folder_name,
                                              paste0(Scheme$folder_name, ".tmp")))
      
      # Find the difference (extra files in local database)
      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
      
      # Copy extra files to temporary folder
      file.copy(file.path(Startup$database,
                          Scheme$folder_name, 
                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
                file.path(Startup$database,
                          Scheme$folder_name,
                          paste0(Scheme$folder_name, ".tmp")))
      
      # Check differences in file pairs
      local_db_hashes <- tools::md5sum(file.path(Startup$database,
                                                 Scheme$folder_name,
                                                 paste0(Scheme$folder_name, "_alleles"),
                                                 local_db_filelist))
      tmp_db_hashes <- tools::md5sum(file.path(Startup$database,
                                               Scheme$folder_name,
                                               paste0(Scheme$folder_name, ".tmp"),
                                               local_db_filelist))
      
      diff_files <- local_db_hashes %in% tmp_db_hashes
      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
      
      # Check locus hashes
      for (locus in diff_loci) {
        local_db_hashes <- get_locus_hashes(file.path(Startup$database,
                                                      Scheme$folder_name,
                                                      paste0(Scheme$folder_name, "_alleles"),
                                                      locus))
        tmp_db_hashes <- get_locus_hashes(file.path(Startup$database,
                                                    Scheme$folder_name,
                                                    paste0(Scheme$folder_name, ".tmp"),
                                                    locus))
        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
        
        sequences <- extract_seq(file.path(Startup$database,
                                           Scheme$folder_name,
                                           paste0(Scheme$folder_name, "_alleles"),
                                           locus), diff_hashes)
        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
            length(sequences$idx) == length(sequences$seq)) {
          add_new_sequences(file.path(Startup$database,
                                      Scheme$folder_name,
                                      paste0(Scheme$folder_name, ".tmp"),
                                      locus), sequences)
        }
      }
    }
    
    unlink(file.path(Startup$database, Scheme$folder_name, 
                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
    
    file.rename(file.path(Startup$database, Scheme$folder_name,
                          paste0(Scheme$folder_name, ".tmp")),
                file.path(Startup$database, Scheme$folder_name,
                          paste0(Scheme$folder_name, "_alleles")))
    
    # Download Scheme Info (pubMLST already downloaded)
    if(grepl("_CM", input$select_cgmlst)) {
      tryCatch(
        {
          scheme_overview <- read_html(Scheme$link_scheme) %>%
            html_table(header = FALSE) %>%
            as.data.frame(stringsAsFactors = FALSE)
          
          names(scheme_overview) <- c("X1", "X2")
          
          scheme_overview <- add_row(scheme_overview,
                                     data.frame(
                                       X1 = c("URL", "Database"), 
                                       X2 = c(
                                         paste0('<a href="', 
                                                schemes$url[schemes$species == input$select_cgmlst], 
                                                '/" target="_blank">', 
                                                schemes$url[schemes$species == input$select_cgmlst], 
                                                '</a>'),
                                         "cgMLST.org Nomenclature Server (h25)")),
                                     .after = 1)
          
          names(scheme_overview) <- NULL
          
          saveRDS(scheme_overview, file.path(Startup$database, Scheme$folder_name, "scheme_info.rds"))
          
          message("Scheme info downloaded")
        },
        error = function(e) {
          stop("Failed to download scheme info: ", "\nError: ", e$message)
        }
      )
    }
    
    available <- gsub("_", " ", basename(dir_ls(Startup$database)))
    DB$available <- available[available %in% gsub("_", " ", schemes$species)]
    DB$exist <- length(dir_ls(Startup$database)) == 0
    
    shinyjs::show("download_cgMLST")
    shinyjs::hide("hashing")
    
    output$statustext <- renderUI(
      fluidRow(
        tags$li(
          class = "dropdown", 
          tags$span(HTML(
            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
            style = "color:white;")
        )
      )
    )
    
    log_print("Download successful")
    
    showModal(
      div(
        class = "load-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'Scheme successfully downloaded.',
                    '</span>'
                  )
                )
              ),
              div(
                class = "modal-element",
                selectInput(
                  "scheme_db",
                  label = "",
                  choices = if(!is.null(Typing$last_scheme)) {
                    Typing$last_scheme
                  } else {DB$available},
                  selected = if(!is.null(Typing$last_scheme)) {
                    Typing$last_scheme
                  } else {if(!is.null(DB$scheme)) {gsub("_", " ", input$select_cgmlst)} else {DB$available[1]}}
                )
              )
            ),
            br()
          ),
          title = "Load Database",
          footer = tagList(
            actionButton("load", "Load", class = "load-db", width = "100px")
          )
        )
      )
    )
    
    # Disable pickerInput
    shinyjs::runjs("$('#select_cgmlst').prop('disabled', false);")
    shinyjs::runjs("$('#select_cgmlst').selectpicker('refresh');")  
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  
  # Download Target Info (CSV Table)
  observe({
    req(input$select_cgmlst, Scheme$link_scheme)
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    input$download_cgMLST
    
    ifelse(length(DB$new_database) > 0,
           database <- DB$new_database,
           database <- Startup$database)
    
    if(dir.exists(file.path(database, input$select_cgmlst))) {
      updateActionButton(session, "download_cgMLST", label = "Fetch Update")
    } else {
      updateActionButton(session, "download_cgMLST", label = "Download")
    }
    
    if(grepl("_CM", input$select_cgmlst)) {
      
      scheme_overview <- tryCatch({
        read_html(Scheme$link_scheme)
      }, error = function(e) {
        DB$failCon <- TRUE
        show_toast(
          title = "Could not retrieve data. Check internet connection.",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
        warning("Could not retrieve data. Check internet connection.")
        return(NULL)
      })
      
      if(!is.null(scheme_overview)) {
        DB$failCon <- FALSE
        scheme_overview <- scheme_overview %>%
          html_table(header = FALSE) %>%
          as.data.frame(stringsAsFactors = FALSE)
        
        names(scheme_overview) <- c("X1", "X2")
        
        scheme_overview <- add_row(scheme_overview,
                                   data.frame(
                                     X1 = c("URL", "Database"), 
                                     X2 = c(
                                       paste0('<a href="', 
                                              schemes$url[schemes$species == input$select_cgmlst], 
                                              '/" target="_blank">', 
                                              schemes$url[schemes$species == input$select_cgmlst], 
                                              '</a>'),
                                       "cgMLST.org Nomenclature Server (h25)")),
                                   .after = 1)
        
        last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
                                       format = "%B %d, %Y, %H:%M %p")
        names(scheme_overview) <- NULL
        
        last_file_change <- format(
          file.info(file.path(Startup$database, ".downloaded_schemes",
                              paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
      }
    } else if(grepl("_PM", input$select_cgmlst)) {
      
      scheme_overview <- tryCatch({
        get.schemeinfo(url_link = schemes$url[schemes$species == input$select_cgmlst])
      }, error = function(e) {
        DB$failCon <- TRUE
        
        show_toast(
          title = "Could not retrieve data. Check internet connection.",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
        warning("Could not retrieve data. Check internet connection.")
        return(NULL)
      })
      
      if(!is.null(scheme_overview)) {
        DB$failCon <- FALSE
        
        if(!is.null(scheme_overview[["last_updated"]])) {
          last_scheme_change <- scheme_overview[["last_updated"]]
          last_file_change <- format(
            file.info(file.path(Startup$database, ".downloaded_schemes",
                                paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
        } else {
          last_scheme_change <- "Not Available"
          last_file_change <- NULL
        }
        
        if(!is.null(scheme_overview[["description"]])) {
          description <- scheme_overview[["description"]]
        } else {
          description <- "Not Available"
        }
        
        scheme_overview <- data.frame(x1 = c("Scheme", "Database", "URL", "Version", "Locus Count", "Last Change"),
                                      x2 = c(gsub("_", " ", Scheme$folder_name),
                                             "pubMLST",
                                             paste0('<a href="', 
                                                    paste0("https://www.pubmlst.org/bigsdb?db=",
                                                           basename(dirname(dirname(schemes$url[schemes$species == input$select_cgmlst])))), 
                                                    '" target="_blank">', 
                                                    paste0("https://www.pubmlst.org/bigsdb?db=",
                                                           basename(dirname(dirname(schemes$url[schemes$species == input$select_cgmlst])))), 
                                                    '</a>'),
                                             description,
                                             scheme_overview[["locus_count"]], 
                                             last_scheme_change))
        
        names(scheme_overview) <- NULL
      }
    }
    
    if(!is.null(scheme_overview)) {
      
      shinyjs::enable("download_cgMLST")
      
      output$cgmlst_scheme_table <- renderUI(
        addSpinner(
          tableOutput("cgmlst_scheme"),
          spin = "dots",
          color = "#ffffff"
        )
      )
      
      # Render scheme info table
      output$cgmlst_scheme <- renderTable({
        scheme_overview
      }, sanitize.text.function = function(x) x,
      width = "90%") 
      
      # Render scheme update availability info
      output$scheme_update_info <- renderUI({
        req(last_file_change, last_scheme_change)
        new_scheme <- last_file_change < last_scheme_change
        if(length(new_scheme) != 0) {
          if(new_scheme) {
            HTML(
              paste0(
                '<i class="fa-solid fa-circle-exclamation" style="font-size:20px;color:orange; position:relative; top: 17px; left: -10px;"></i>',
                '<span style="color: white; font-size: 15px; position:relative; top: 15px;">',
                "Updated scheme available",
                '</span>'
              )
            )
          } else {
            HTML(
              paste0(
                '<i class="fa-solid fa-check" style="font-size:20px;color:lightgreen; position:relative; top: 17px; left: -10px;"></i>',
                '<span style="color: white; font-size: 15px; position:relative; top: 15px;">',
                "Scheme is up-to-date",
                '</span>'
              )
            )
          }
        }
      })
      
      #output$cgmlst_scheme_no_con <- NULL
    } else {
      
      shinyjs::disable("download_cgMLST")
      
      output$cgmlst_scheme <- NULL
      output$scheme_update_info <- NULL
      output$test <- renderUI(
        HTML(
          paste(
            '<i class="fas fa-triangle-exclamation" style="font-size:15px; color: yellow;" ></i>',
            '<span style="color: white; font-size: 15px;">',
            "&nbsp Failed to fetch data. Check internet connection and try again.")
        )
      )
    }
    
    ### Render species info
    selected_species <- gsub("_", " ", gsub("_(PM|CM)", "", schemes$species[schemes$species == input$select_cgmlst]))
    
    tryCatch({
      Scheme$species_data <- fetch.species.data(species = selected_species)
    }, error = function(e) {
      DB$failCon <- TRUE
      show_toast(
        title = "Could not retrieve data. Check internet connection.",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
      warning("Could not retrieve data. Check internet connection.")
      Scheme$species_data <- NULL
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ### Render species info & image ----
  observe({
    req(Scheme$species_data)
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    DB$failCon <- FALSE
    
    multiple <- length(Scheme$species_data) > 1 & !is.null(input$selected_species)
    if(multiple) {
      species_data <- Scheme$species_data[[input$selected_species]]
    } else {
      species_data <- Scheme$species_data[[1]]
    }
    
    if(!is.null(species_data)) {
      
      # Download and render species image
      if(length(Scheme$species_data) > 1 & length(Scheme$species_data) > 0) {
        if(!is.null(input$selected_species)) {
          # Download image
          destination_file <- file.path(Startup$database, 
                                        schemes$species[schemes$species == input$select_cgmlst], 
                                        paste0(input$selected_species, ".jpg"))
          if(!dir.exists(dirname(destination_file))) {
            if(file.exists(file.path(tempdir(), paste0(input$selected_species, ".jpg")))) {
              destination_file <- file.path(tempdir(), paste0(input$selected_species, ".jpg"))      
              output$species_no_img <- NULL
              output$species_img <- renderImage({
                list(src = destination_file,
                     height = 180)
              }, deleteFile = FALSE)
            } else {
              if(!is.null(Scheme$species_data[[input$selected_species]])) {
                response <- httr::GET(Scheme$species_data[[input$selected_species]]$Image)
                destination_file <- file.path(tempdir(), paste0(input$selected_species, ".jpg")) 
                if (response$status_code == 200) {
                  writeBin(httr::content(response, "raw"), destination_file)
                  response <- NULL
                  output$species_no_img <- NULL
                  output$species_img <- renderImage({
                    list(src = destination_file,
                         height = 180)
                  }, deleteFile = FALSE)
                  print("Image downloaded successfully!")
                } else {
                  output$species_img <- NULL
                  output$species_no_img <- renderUI(
                    HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
                  )
                  print("Failed to download image.")
                }
              } 
            }
          } else {
            if(!file.exists(destination_file)) {
              if(!is.null(Scheme$species_data[[input$selected_species]])) {
                response <- httr::GET(Scheme$species_data[[input$selected_species]]$Image)
                destination_file <- file.path(tempdir(), paste0(input$selected_species, ".jpg")) 
                
                if (response$status_code == 200) {
                  writeBin(httr::content(response, "raw"), destination_file)
                  response <- NULL
                  print("Image downloaded successfully!")
                  output$species_no_img <- NULL
                  output$species_img <- renderImage({
                    list(src = destination_file,
                         height = 180)
                  }, deleteFile = FALSE)
                } else {
                  output$species_no_img <- renderUI(
                    HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
                  )
                  output$species_img <- NULL
                  print("Failed to download image.")
                }
              }
            } else {
              output$species_no_img <- NULL
              output$species_img <- renderImage({
                list(src = destination_file,
                     height = 180)
              }, deleteFile = FALSE)
            }
          }
        }
      } else if(length(Scheme$species_data) > 0) {
        
        # Download image
        destination_file <- file.path(Startup$database, 
                                      schemes$species[schemes$species == input$select_cgmlst], 
                                      paste0(schemes$species[schemes$species == input$select_cgmlst], ".jpg"))
        
        if(!dir.exists(dirname(destination_file))) {
          if(file.exists(file.path(tempdir(), paste0(schemes$species[schemes$species == input$select_cgmlst], ".jpg")))) {
            
            destination_file <- file.path(tempdir(), paste0(schemes$species[schemes$species == input$select_cgmlst], ".jpg"))      
            output$species_no_img <- NULL
            output$species_img <- renderImage({
              list(src = destination_file,
                   height = 180)
            }, deleteFile = FALSE)
          } else {
            destination_file <- file.path(tempdir(), paste0(schemes$species[schemes$species == input$select_cgmlst], ".jpg")) 
            response <- httr::GET(Scheme$species_data[[1]]$Image)
            if (response$status_code == 200) {
              writeBin(httr::content(response, "raw"), destination_file)
              output$species_no_img <- NULL
              output$species_img <- renderImage({
                list(src = destination_file,
                     height = 180)
              }, deleteFile = FALSE)
              print("Image downloaded successfully!")
            } else {
              output$species_img <- NULL
              output$species_no_img <- renderUI(
                HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
              )
              print("Failed to download image.")
            }
          }
        } else {
          if(!file.exists(destination_file)) {
            response <- httr::GET(Scheme$species_data[[1]]$Image)
            
            if (response$status_code == 200) {
              writeBin(httr::content(response, "raw"), destination_file)
              print("Image downloaded successfully!")
              output$species_no_img <- NULL
              output$species_img <- renderImage({
                list(src = destination_file,
                     height = 180)
              }, deleteFile = FALSE)
            } else {
              output$species_img <- NULL
              output$species_no_img <- renderUI(
                HTML('<i class="fa-solid fa-bacteria" style="font-size:150px;color:white;margin-right:25px;" ></i>')
              )
              print("Failed to download image.")
            }
          } else {
            output$species_no_img <- NULL
            output$species_img <- renderImage({
              list(src = destination_file,
                   height = 180)
            }, deleteFile = FALSE)
          }
        }
      }
      
      # Render species info
      output$species_info <- renderUI({
        addSpinner(
          box(
            solidHeader = TRUE,
            status = "primary",
            width = "100%",
            title = HTML(
              paste0(
                '<span style="color: white; font-size: 15px;">',
                'Species Information - Data Fetched from NCBI&nbsp&nbsp&nbsp ',
                ' <a href="', 'https://www.ncbi.nlm.nih.gov/' , '" target="_blank" style="color:#008edb; font-style:normal; text-decoration:none;"> https://www.ncbi.nlm.nih.gov/ </a>',
                '</span>'
              )
            ),
            column(
              width = 12,
              fluidRow(
                br(),
                column(
                  width = 7,
                  p(
                    HTML(
                      paste0(
                        '<i class="fa-solid fa-bacterium" style="font-size:20px;color:white; margin-right: 10px;"></i>',
                        '<span style="color: white; font-size: 22px; ">',
                        species_data$Name$name,
                        '</span>'
                      )
                    )
                  ),
                  p(
                    HTML(
                      paste0(
                        '<span style="color: white; font-size: 12px;">',
                        species_data$Name$authority,
                        '</span>'
                      )
                    )
                  ),
                  br(),
                  p(
                    HTML(
                      paste0(
                        '<span style="color: white; font-size: 15px;">',
                        'URL: ',
                        '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                        species_data$ID,
                        '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                        species_data$Name$name,
                        ' NCBI',
                        '</a>',
                        '</span>'
                      )
                    )
                  ),
                  br(),
                  fluidRow(
                    column(
                      width = 12,
                      p(
                        HTML(
                          paste0(
                            '<i class="fa-solid fa-sitemap" style="font-size:20px;color:white; margin-right: 10px;"></i>',
                            '<span style="color: white; font-size: 20px;">',
                            'Lineage', '</span>'
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$superkingdom$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$superkingdom$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          align = "left",
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Superkingdom',
                                '</span>'
                              )
                            )
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$phylum$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$phylum$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Phylum',
                                '</span>'
                              )
                            )
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$class$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$class$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          align = "left",
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Class',
                                '</span>'
                              )
                            )
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$order$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$order$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          align = "left",
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Order',
                                '</span>'
                              )
                            )
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$family$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$family$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          align = "left",
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Family',
                                '</span>'
                              )
                            )
                          )
                        )
                      ),
                      fluidRow(
                        column(
                          width = 6,
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 15px;">',
                                '<a href="https://www.ncbi.nlm.nih.gov/datasets/taxonomy/',
                                species_data$Classification$genus$id,
                                '/" target="_blank" style="color:#008edb; text-decoration:none;">',
                                species_data$Classification$genus$name,
                                '</a>',
                                '</span>'
                              )
                            )
                          )
                        ),
                        column(
                          width = 6,
                          align = "left",
                          p(
                            HTML(
                              paste0(
                                '<span style="color: white; font-size: 12px;">',
                                'Genus',
                                '</span>'
                              )
                            )
                          )
                        )
                      )
                    )
                  )
                ),
                column(
                  width = 5,
                  align = "right",
                  uiOutput("species_no_img"),
                  div( 
                    class = "species-image",
                    imageOutput("species_img", width = "300px", height = "200px")
                  )
                )
              )
            )
          ),
          spin = "dots",
          color = "#ffffff"
        )
      })
    } else {
      output$species_info <- NULL
      output$species_img <- NULL
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Species info selector UI
  observe({
    if(!is.null(Scheme$species_data)) {
      if(length(Scheme$species_data) > 1) {
        choices <- gsub(" ", "_", unlist(lapply(Scheme$species_data, function(x) x$Name$name)))
        names(choices) <- gsub("_", " ", unlist(lapply(Scheme$species_data, function(x) x$Name$name)))
        output$species_info_select <- renderUI({
          fluidRow(
            column(1),
            column(
              width = 3,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; font-size: 15px; position: relative; top: 5px;">',
                    'Species Complex',
                    '</span>'
                  )
                )
              )
            ),
            column(
              width = 1,
              bslib::tooltip(
                bsicons::bs_icon("question-circle", 
                                 title = "Scheme comprises multiple species.", 
                                 color = "white", height = "14px", width = "14px", 
                                 position = "relative", top = "9px", right = "28px"),
                "Text shown in the tooltip.",
                show = FALSE,
                id = "schemeinfo_tooltip"
              )
            ),
            column(
              width = 6,
              div(
                class = "selected-species",
                selectInput(
                  "selected_species",
                  "",
                  choices = choices
                )
              )
            )
          )
        })
      } else {
        output$species_info_select <- NULL
      }
    } else {
      output$species_info_select <- NULL
    }
  })
  
  # Switch to Manage Schemes tab if user wants to update scheme
  observeEvent(input$update_scheme, {
    removeModal()
    updateTabItems(session, "tabs", selected = "init")
  })
  
  # _______________________ ####
  
  ## Visualization ----
  
  # Render placeholder image
  
  output$placeholder <- renderImage({
    # Path to your PNG image with a transparent background
    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
    
    # Use HTML to display the image with the <img> tag
    list(src = image_path,
         height = 180)
  }, deleteFile = FALSE)
  
  
  ### Plot Controls ----
  
  tree_type_reactive <- reactiveVal()
  
  observe({
    if(!is.null(input$tree_type)) {
      tree_type_reactive(input$tree_type)
    } else {
      tree_type_reactive("MST")
    }
  })
  
  output$generate_plot_ui <- renderUI({
    
    box(
      solidHeader = TRUE,
      status = "primary",
      width = "100%",
      title = plot.control(),
      fluidRow(
        column(
          width = 8,
          fluidRow(
            column(
              width = 6,
              div(
                class = "tree-info",
                popify(
                  div(id = "tree_info_icon",
                      HTML('<i class="fa-regular fa-circle-question" style="color: white !important; top: -38px; position: absolute; font-size: 16px; padding: 5px; left: 74px"></i>')),
                  gsub("Generate ", "", plot.control()),
                  tree.type.info(),
                  options=list(container="body"))
              ),
              radioGroupButtons(
                inputId = "tree_type",
                label = "", 
                choices = c("MST", "Tree"),
                selected = tree_type_reactive(),
                justified = TRUE
              )
            ),
            uiOutput("tree_algo_lines"),
            column(
              width = 4,
              uiOutput("tree_algo_ui")
            )
          )
        ),
        column(
          width = 4,
          tags$div(
            id = "button-wrapper",
            actionButton(
              "create_tree",
              h5("Generate", style = "position: relative; left: 15px; color: white; font-size: 15px;"),
              width = "100%"
            ),
            tags$img(
              src = "phylo.png",
              alt = "icon",
              class = "icon"
            )
          )
        )
      )
    )
  })
  
  output$tree_algo_ui <- renderUI({
    tree_algo <- prettyRadioButtons(
      inputId = "tree_algo",
      "",
      choices = c("Neighbour-Joining", "UPGMA"),
      inline = FALSE
    )
    
    if(tree_type_reactive() == "MST") {
      shinyjs::disabled(tree_algo)
    } else {
      tree_algo
    }
  })
  
  output$tree_algo_lines <- renderUI({
    if(tree_type_reactive() == "MST") {
      div(
        div(class = "lower-line-inactive"),
        div(class = "upper-line-inactive")
      )
    } else {
      div(
        div(class = "lower-line-active"),
        div(class = "upper-line-active")
      )
    }
  })
  
  
  #### Tree controls ----
  
  # Initially shown label menu
  
  session$sendCustomMessage('nj_highlight', "nj_label_menu")
  
  output$tree_controls <- renderUI(
    div(
      class = "control-box",
      box(
        solidHeader = TRUE,
        status = "primary",
        width = "100%",
        title = "Labels",
        fluidRow(
          div(
            class = "nj-label-control-col",
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                column(
                  width = 6,
                  align = "left",
                  h4(p("Isolate Label"), style = "color:white; position: relative; right: -15px; "),   
                ),
                column(
                  width = 6,
                  align = "left",
                  div(
                    class = "mat-switch-lab",
                    materialSwitch(
                      "nj_tiplab_show",
                      "",
                      value = TRUE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 9,
                  align = "left",
                  div(
                    class = "nj-label-sel",
                    uiOutput("nj_tiplab_ui")
                  )   
                ),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    actionBttn(
                      "nj_labeltext_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 6,
                        align = "center",
                        uiOutput("nj_align_ui"),
                        br(),
                        sliderInput(
                          "nj_tiplab_size",
                          label = h5("Label size", style = "color:white; margin-bottom: 0px"),
                          min = 1,
                          max = 10,
                          step = 0.5,
                          value = nj_tiplab_size_val(),
                          width = "150px",
                          ticks = FALSE
                        ),
                        br(),
                        sliderInput(
                          "nj_tiplab_alpha",
                          label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                          min = 0.1,
                          max = 1,
                          step = 0.05,
                          value = 1,
                          width = "150px",
                          ticks = FALSE
                        )
                      ),
                      column(
                        width = 6,
                        align = "center",
                        selectInput(
                          "nj_tiplab_fontface",
                          label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
                          width = "250px",
                          choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic"),
                          selected = "plain"
                        ),
                        br(),
                        sliderInput(
                          inputId = "nj_tiplab_position",
                          label = h5("Position", style = "color:white; margin-bottom: 0px"),
                          min = -3,
                          max = 3,
                          step = 0.05,
                          value = 0,
                          width = "150px",
                          ticks = FALSE
                        ) , 
                        br(),
                        uiOutput("nj_tiplab_angle_ui")     
                      )
                    )
                  )
                )
              )
            )
          )
        ),
        fluidRow(
          column(
            width = 8,
            div(
              class = "mat-switch-geom",
              materialSwitch(
                "nj_geom",
                h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: 5px;"),
                value = FALSE,
                right = FALSE
              )
            )
          ),
          column(
            width = 4,
            dropMenu(
              actionBttn(
                "nj_labelformat_menu",
                label = "",
                color = "default",
                size = "sm",
                style = "material-flat",
                icon = icon("sliders")
              ),
              placement = "right",
              theme = "translucent",
              fluidRow(
                column(
                  width = 12,
                  align = "center",
                  sliderInput(
                    inputId = "nj_tiplab_padding",
                    label = h5("Size", style = "color:white; margin-bottom: 0px"),
                    min = 0.05,
                    max = 1,
                    value = nj_tiplab_padding_val(),
                    step = 0.05,
                    width = "150px",
                    ticks = FALSE
                  ),
                  br(),
                  sliderInput(
                    inputId = "nj_tiplab_labelradius",
                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
                    min = 0,
                    step = 0.05,
                    max = 0.5,
                    value = 0.2,
                    width = "150px",
                    ticks = FALSE
                  )
                )
              )
            )
          )
        ),
        hr(),
        fluidRow(
          div(
            class = "nj-label-control-col",
            column(
              width = 12,
              align = "left",
              fluidRow(
                column(
                  width = 6,
                  align = "left",
                  h4(p("Branches"), style = "color:white; position: relative; right: -15px;"),
                ),
                column(
                  width = 6,
                  align = "left",
                  div(
                    class = "mat-switch-lab",
                    materialSwitch(
                      "nj_show_branch_label",
                      "",
                      value = FALSE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 9,
                  align = "left",
                  div(
                    class = "nj-label-sel",
                    uiOutput("nj_branch_label")
                  )   
                ),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    actionBttn(
                      "nj_branch_label_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 6,
                        align = "center",
                        selectInput(
                          "nj_branchlab_fontface",
                          label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
                          width = "250px",
                          choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
                        ),
                        br(),
                        sliderInput(
                          inputId = "nj_branch_x",
                          label = h5("X Position", style = "color:white; margin-bottom: 0px"),
                          min = -3,
                          max = 3,
                          value = 0,
                          width = "250px",
                          ticks = FALSE
                        ),
                        br(),
                        sliderInput(
                          "nj_branchlab_alpha",
                          label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                          min = 0.1,
                          max = 1,
                          step = 0.05,
                          value = 0.65,
                          width = "250px",
                          ticks = FALSE
                        )
                      ),
                      column(
                        width = 6,
                        align = "center",
                        sliderInput(
                          "nj_branch_size",
                          label = h5("Size", style = "color:white; margin-bottom: 0px"),
                          min = 2,
                          max = 10,
                          step = 0.5,
                          value = nj_branch_size_val(),
                          width = "150px",
                          ticks = FALSE
                        ),
                        br(),
                        sliderInput(
                          "nj_branch_labelradius",
                          label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
                          min = 0,
                          max = 0.5,
                          step = 0.05,
                          value = 0.5,
                          width = "250px",
                          ticks = FALSE
                        )
                      )
                    )
                  )
                )
              )
            )
          )
        ),
        hr(),
        fluidRow(
          column(
            width = 12,
            align = "left",
            fluidRow(
              column(
                width = 8,
                textInput(
                  "nj_title",
                  label = "",
                  width = "100%",
                  placeholder = "Plot Title"
                )
              ),
              column(
                width = 4,
                dropMenu(
                  actionBttn(
                    "nj_title_menu",
                    label = "",
                    color = "default",
                    size = "sm",
                    style = "material-flat",
                    icon = icon("sliders")
                  ),
                  placement = "right",
                  theme = "translucent",
                  fluidRow(
                    column(
                      width = 12,
                      align = "center",
                      sliderInput(
                        "nj_title_size",
                        label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
                        value = 30,
                        min = 15,
                        max = 40,
                        step = 1,
                        width = "150px",
                        ticks = FALSE
                      )
                    )
                  )
                )
              )
            )
          )
        ),
        br(),
        fluidRow(
          column(
            width = 12,
            align = "left",
            fluidRow(
              column(
                width = 8,
                textInput(
                  "nj_subtitle",
                  label = "",
                  width = "100%",
                  placeholder = "Plot Subtitle"
                )
              ),
              column(
                width = 4,
                dropMenu(
                  actionBttn(
                    "nj_subtitle_menu",
                    label = "",
                    color = "default",
                    size = "sm",
                    style = "material-flat",
                    icon = icon("sliders")
                  ),
                  placement = "right",
                  theme = "translucent",
                  fluidRow(
                    column(
                      width = 12,
                      align = "center",
                      sliderInput(
                        "nj_subtitle_size",
                        label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
                        value = 30,
                        min = 15,
                        max = 40,
                        step = 1,
                        width = "150px",
                        ticks = FALSE
                      )
                    )
                  )
                )
              )
            )
          )
        ),
        hr(),
        fluidRow(
          div(
            class = "nj-label-control-col",
            column(
              width = 12,
              align = "left",
              h4(p("Custom Label"), style = "color:white; position: relative; right: -15px;"),
              column(
                width = 12,
                align = "center",
                fluidRow(
                  column(
                    width = 7,
                    textInput(
                      "nj_new_label_name",
                      "",
                      placeholder = "New Label"
                    )
                  ),
                  column(
                    width = 3,
                    actionButton(
                      "nj_add_new_label",
                      "",
                      icon = icon("plus")
                    )
                  ),
                  column(
                    width = 2,
                    align = "right",
                    dropMenu(
                      actionBttn(
                        "nj_custom_label_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right",
                      theme = "translucent",
                      fluidRow(
                        div(
                          class = "nj-custom-label-menu-col",
                          column(
                            width = 12,
                            align = "center",
                            fluidRow(
                              column(
                                width = 3,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                              'Size')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  uiOutput("nj_custom_labelsize")
                                )
                              )
                            ),
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                              'Vertical')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  uiOutput("nj_sliderInput_y")
                                )
                              )
                            ),
                            br(),
                            fluidRow(
                              column(
                                width = 3,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                              'Horizontal')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  uiOutput("nj_sliderInput_x")
                                )
                              )
                            )
                          )
                        )
                      )
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 7,
                    uiOutput("nj_custom_label_select")
                  ),
                  column(
                    width = 4,
                    actionButton(
                      "nj_del_label",
                      "",
                      icon = icon("minus")
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 12,
                    align = "center",
                    actionButton(
                      "nj_cust_label_save",
                      "Apply"
                    )
                  )
                )
              )
            )
          )
        )
      ) 
    )
  )
  
  
  ##### Label Menu ----
  
  ###### Label Control Values ----
  
  # Tip label
  nj_tiplab_reactive <- reactive({
    ifelse(!is.null(input$nj_tiplab),
           input$nj_tiplab,
           "Assembly Name")}) |> debounce(100)
  nj_tiplab_val <- reactiveVal()
  nj_tiplab_show_val <- reactiveVal()
  nj_align_reactive <- reactive({
    ifelse(!is.null(input$nj_align),
           input$nj_align,
           FALSE)}) |> debounce(100)
  nj_align_val <- reactiveVal()
  nj_tiplab_size_val <- reactiveVal()
  nj_tiplab_fontface_val <- reactiveVal()
  nj_tiplab_alpha_val <- reactiveVal()
  nj_tiplab_position_val <- reactiveVal()
  nj_tiplab_angle_val <- reactiveVal()
  
  observe({
    nj_tiplab_val(nj_tiplab_reactive())
    
    ifelse(!is.null(input$nj_tiplab_show),
           nj_tiplab_show_val(input$nj_tiplab_show),
           nj_tiplab_show_val(TRUE))
    
    ifelse(!is.null(Vis$tree_algo),
           ifelse(Vis$tree_algo == "UPGMA",
                  nj_align_val(TRUE),
                  nj_align_val(nj_align_reactive())),
           nj_align_val(nj_align_reactive()))
    
    ifelse(!is.null(input$nj_tiplab_size),
           nj_tiplab_size_val(input$nj_tiplab_size),
           ifelse(!is.null(Vis$labelsize_nj),
                  nj_tiplab_size_val(Vis$labelsize_nj),
                  nj_tiplab_size_val(4)))
    
    ifelse(!is.null(input$nj_tiplab_fontface),
           nj_tiplab_fontface_val(input$nj_tiplab_fontface),
           nj_tiplab_fontface_val("plain"))
    
    ifelse(!is.null(input$nj_tiplab_alpha),
           nj_tiplab_alpha_val(input$nj_tiplab_alpha),
           nj_tiplab_alpha_val(1))
    
    ifelse(!is.null(input$nj_tiplab_position),
           nj_tiplab_position_val(input$nj_tiplab_position),
           ifelse(!is.null(nj_layout_val()),
                  ifelse(nj_layout_val() != "inward" & 
                           nj_layout_val() != "circular",
                         nj_tiplab_position_val(0),
                         ifelse(nj_layout_val() == "inward",
                                nj_tiplab_position_val(1.1),
                                nj_tiplab_position_val(-0.05))),
                  nj_tiplab_position_val(0)))
    
    ifelse(!is.null(input$nj_tiplab_angle),
           nj_tiplab_angle_val(input$nj_tiplab_angle),
           nj_tiplab_angle_val(0))
  })
  
  # Label panels
  nj_geom_val <- reactiveVal()
  nj_tiplab_labelradius_val <- reactiveVal()
  nj_tiplab_padding_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_geom),
           nj_geom_val(input$nj_geom),
           nj_geom_val(FALSE))
    
    ifelse(!is.null(input$nj_tiplab_labelradius),
           nj_tiplab_labelradius_val(input$nj_tiplab_labelradius),
           nj_tiplab_labelradius_val(0.2))
    
    ifelse(!is.null(input$nj_tiplab_padding),
           nj_tiplab_padding_val(input$nj_tiplab_padding),
           ifelse(!is.null(Vis$tiplab_padding_nj),
                  nj_tiplab_padding_val(Vis$tiplab_padding_nj),
                  nj_tiplab_padding_val(0.2)))
  })
  
  # Branch labels
  nj_show_branch_label_val <- reactiveVal()
  nj_branch_size_val <- reactiveVal()
  nj_branch_label_reactive <- reactive({
    ifelse(!is.null(input$nj_branch_label),
           input$nj_branch_label,
           "Host")}) |> debounce(100)
  nj_branch_label_val <- reactiveVal()
  nj_branchlab_alpha_val <- reactiveVal()
  nj_branch_x_val <- reactiveVal()
  nj_branchlab_fontface_val <- reactiveVal()
  nj_branch_labelradius_val <- reactiveVal()

  observe({
    ifelse(!is.null(input$nj_show_branch_label),
           nj_show_branch_label_val(input$nj_show_branch_label),
           nj_show_branch_label_val(FALSE))
    
    ifelse(!is.null(input$nj_branch_size),
           nj_branch_size_val(input$nj_branch_size),
           ifelse(!is.null(Vis$branch_size_nj),
                  nj_branch_size_val(Vis$branch_size_nj),
                  nj_branch_size_val(4)))
    
    nj_branch_label_val(nj_branch_label_reactive())
    
    ifelse(!is.null(input$nj_branchlab_alpha),
           nj_branchlab_alpha_val(input$nj_branchlab_alpha),
           nj_branchlab_alpha_val(0.65))
    
    ifelse(!is.null(input$nj_branch_x),
           nj_branch_x_val(input$nj_branch_x),
           nj_branch_x_val(0))
    
    ifelse(!is.null(input$nj_branchlab_fontface),
           nj_branchlab_fontface_val(input$nj_branchlab_fontface),
           nj_branchlab_fontface_val("plain"))
    
    ifelse(!is.null(input$nj_branch_labelradius),
           nj_branch_labelradius_val(input$nj_branch_labelradius),
           nj_branch_labelradius_val(0.5))
  })
  
  # Titles
  nj_title_val <- reactiveVal()
  nj_title_size_val <- reactiveVal()
  nj_subtitle_val <- reactiveVal()
  nj_subtitle_size_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_title),
           nj_title_val(input$nj_title),
           nj_title_val(NULL))
    
    ifelse(!is.null(input$nj_title_size),
           nj_title_size_val(input$nj_title_size),
           nj_title_size_val(30))
    
    ifelse(!is.null(input$nj_subtitle),
           nj_subtitle_val(input$nj_subtitle),
           nj_subtitle_val(NULL))
    
    ifelse(!is.null(input$nj_subtitle_size),
           nj_subtitle_size_val(input$nj_subtitle_size),
           nj_subtitle_size_val(30))
  })
  
  ###### Label Interface ----
  
  observeEvent(input$nj_label_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_label_menu")
    
    output$tree_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Labels",
          fluidRow(
            div(
              class = "nj-label-control-col",
              column(
                width = 12,
                align = "left",
                br(),
                fluidRow(
                  column(
                    width = 6,
                    align = "left",
                    h4(p("Isolate Label"), style = "color:white; position: relative; right: -15px; "),   
                  ),
                  column(
                    width = 6,
                    align = "left",
                    div(
                      class = "mat-switch-lab",
                      materialSwitch(
                        "nj_tiplab_show",
                        "",
                        value = isolate(nj_tiplab_show_val())
                      )
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 9,
                    align = "left",
                    div(
                      class = "nj-label-sel",
                      uiOutput("nj_tiplab_ui")
                    )   
                  ),
                  column(
                    width = 3,
                    align = "center",
                    dropMenu(
                      actionBttn(
                        "nj_labeltext_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right",
                      theme = "translucent",
                      fluidRow(
                        column(
                          width = 6,
                          align = "center",
                          uiOutput("nj_align_ui"),
                          br(),
                          sliderInput(
                            "nj_tiplab_size",
                            label = h5("Label size", style = "color:white; margin-bottom: 0px"),
                            min = 1,
                            max = 10,
                            step = 0.5,
                            value = isolate(nj_tiplab_size_val()),
                            width = "150px",
                            ticks = FALSE
                          ),
                          br(),
                          sliderInput(
                            "nj_tiplab_alpha",
                            label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                            min = 0.1,
                            max = 1,
                            step = 0.05,
                            value = isolate(nj_tiplab_alpha_val()),
                            width = "150px",
                            ticks = FALSE
                          )
                        ),
                        column(
                          width = 6,
                          align = "center",
                          selectInput(
                            "nj_tiplab_fontface",
                            label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
                            width = "250px",
                            choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic"),
                            selected = isolate(nj_tiplab_fontface_val())
                          ),
                          br(),
                          sliderInput(
                            inputId = "nj_tiplab_position",
                            label = h5("Position", style = "color:white; margin-bottom: 0px"),
                            min = -3,
                            max = 3,
                            step = 0.05,
                            value = isolate(nj_tiplab_position_val()),
                            width = "150px",
                            ticks = FALSE
                          ),  
                          br(),
                          uiOutput("nj_tiplab_angle_ui")        
                        )
                      )
                    )
                  )
                )
              )
            )
          ),
          fluidRow(
            column(
              width = 8,
              div(
                class = "mat-switch-geom",
                materialSwitch(
                  "nj_geom",
                  h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: 5px;"),
                  value = isolate(nj_geom_val()),
                  right = FALSE
                )
              )
            ),
            column(
              width = 4,
              dropMenu(
                actionBttn(
                  "nj_labelformat_menu",
                  label = "",
                  color = "default",
                  size = "sm",
                  style = "material-flat",
                  icon = icon("sliders")
                ),
                placement = "right",
                theme = "translucent",
                fluidRow(
                  column(
                    width = 12,
                    align = "center",
                    sliderInput(
                      inputId = "nj_tiplab_padding",
                      label = h5("Size", style = "color:white; margin-bottom: 0px"),
                      min = 0.05,
                      max = 1,
                      value = isolate(nj_tiplab_padding_val()),
                      step = 0.05,
                      width = "150px",
                      ticks = FALSE
                    ),
                    br(),
                    sliderInput(
                      inputId = "nj_tiplab_labelradius",
                      label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
                      min = 0,
                      step = 0.05,
                      max = 0.5,
                      value = isolate(nj_tiplab_labelradius_val()),
                      width = "150px",
                      ticks = FALSE
                    )
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            div(
              class = "nj-label-control-col",
              column(
                width = 12,
                align = "left",
                fluidRow(
                  column(
                    width = 6,
                    align = "left",
                    h4(p("Branches"), style = "color:white; position: relative; right: -15px;"),
                  ),
                  column(
                    width = 6,
                    align = "left",
                    div(
                      class = "mat-switch-lab",
                      materialSwitch(
                        "nj_show_branch_label",
                        "",
                        value = isolate(nj_show_branch_label_val())
                      )
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 9,
                    align = "left",
                    div(
                      class = "nj-label-sel",
                      uiOutput("nj_branch_label")
                    )   
                  ),
                  column(
                    width = 3,
                    align = "center",
                    dropMenu(
                      actionBttn(
                        "nj_branch_label_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right",
                      theme = "translucent",
                      fluidRow(
                        column(
                          width = 6,
                          align = "center",
                          selectInput(
                            "nj_branchlab_fontface",
                            label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
                            width = "250px",
                            choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic"),
                            selected = isolate(nj_branchlab_fontface_val())
                          ),
                          br(),
                          sliderInput(
                            inputId = "nj_branch_x",
                            label = h5("X Position", style = "color:white; margin-bottom: 0px"),
                            min = -3,
                            max = 3,
                            value = isolate(nj_branch_x_val()),
                            width = "250px",
                            ticks = FALSE
                          ),
                          br(),
                          sliderInput(
                            "nj_branchlab_alpha",
                            label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                            min = 0.1,
                            max = 1,
                            step = 0.05,
                            value = isolate(nj_branchlab_alpha_val()),
                            width = "250px",
                            ticks = FALSE
                          )
                        ),
                        column(
                          width = 6,
                          align = "center",
                          sliderInput(
                            "nj_branch_size",
                            label = h5("Size", style = "color:white; margin-bottom: 0px"),
                            min = 2,
                            max = 10,
                            step = 0.5,
                            value = isolate(nj_branch_size_val()),
                            width = "150px",
                            ticks = FALSE
                          ),
                          br(),
                          sliderInput(
                            "nj_branch_labelradius",
                            label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
                            min = 0,
                            max = 0.5,
                            step = 0.05,
                            value = isolate(nj_branch_labelradius_val()),
                            width = "250px",
                            ticks = FALSE
                          )
                        )
                      )
                    )
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                column(
                  width = 8,
                  textInput(
                    "nj_title",
                    label = "",
                    width = "100%",
                    placeholder = "Plot Title",
                    value = isolate(nj_title_val())
                  )
                ),
                column(
                  width = 4,
                  dropMenu(
                    actionBttn(
                      "nj_title_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        sliderInput(
                          "nj_title_size",
                          label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
                          value = isolate(nj_title_size_val()),
                          min = 15,
                          max = 40,
                          step = 1,
                          width = "150px",
                          ticks = FALSE
                        )
                      )
                    )
                  )
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                column(
                  width = 8,
                  textInput(
                    "nj_subtitle",
                    label = "",
                    width = "100%",
                    placeholder = "Plot Subtitle",
                    value = isolate(nj_subtitle_val())
                  )
                ),
                column(
                  width = 4,
                  dropMenu(
                    actionBttn(
                      "nj_subtitle_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        sliderInput(
                          "nj_subtitle_size",
                          label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
                          value = isolate(nj_subtitle_size_val()),
                          min = 15,
                          max = 40,
                          step = 1,
                          width = "150px",
                          ticks = FALSE
                        )
                      )
                    )
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            div(
              class = "nj-label-control-col",
              column(
                width = 12,
                align = "left",
                h4(p("Custom Label"), style = "color:white; position: relative; right: -15px;"),
                column(
                  width = 12,
                  align = "center",
                  fluidRow(
                    column(
                      width = 7,
                      textInput(
                        "nj_new_label_name",
                        "",
                        placeholder = "New Label"
                      )
                    ),
                    column(
                      width = 3,
                      actionButton(
                        "nj_add_new_label",
                        "",
                        icon = icon("plus")
                      )
                    ),
                    column(
                      width = 2,
                      align = "right",
                      dropMenu(
                        actionBttn(
                          "nj_custom_label_menu",
                          label = "",
                          color = "default",
                          size = "sm",
                          style = "material-flat",
                          icon = icon("sliders")
                        ),
                        placement = "right",
                        theme = "translucent",
                        fluidRow(
                          div(
                            class = "nj-custom-label-menu-col",
                            column(
                              width = 12,
                              align = "center",
                              fluidRow(
                                column(
                                  width = 3,
                                  align = "left",
                                  HTML(
                                    paste(
                                      tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                                'Size')
                                    )
                                  )
                                ),
                                column(
                                  width = 9,
                                  align = "right",
                                  div(
                                    class = "nj-label-slider",
                                    uiOutput("nj_custom_labelsize")
                                  )
                                )
                              ),
                              br(),
                              fluidRow(
                                column(
                                  width = 3,
                                  align = "left",
                                  HTML(
                                    paste(
                                      tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                                'Vertical')
                                    )
                                  )
                                ),
                                column(
                                  width = 9,
                                  align = "right",
                                  div(
                                    class = "nj-label-slider",
                                    uiOutput("nj_sliderInput_y")
                                  )
                                )
                              ),
                              br(),
                              fluidRow(
                                column(
                                  width = 3,
                                  align = "left",
                                  HTML(
                                    paste(
                                      tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                                'Horizontal')
                                    )
                                  )
                                ),
                                column(
                                  width = 9,
                                  align = "right",
                                  div(
                                    class = "nj-label-slider",
                                    uiOutput("nj_sliderInput_x")
                                  )
                                )
                              )
                            )
                          )
                        )
                      )
                    )
                  ),
                  fluidRow(
                    column(
                      width = 7,
                      uiOutput("nj_custom_label_select")
                    ),
                    column(
                      width = 4,
                      actionButton(
                        "nj_del_label",
                        "",
                        icon = icon("minus")
                      )
                    )
                  ),
                  fluidRow(
                    column(
                      width = 12,
                      align = "center",
                      actionButton(
                        "nj_cust_label_save",
                        "Apply"
                      )
                    )
                  )
                )
              )
            )
          )
        ) 
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ###### Label Inputs ----
  
  # Tip label
  output$nj_tiplab_ui <- renderUI({
    choices <- c(Index = "Index", `Assembly ID` = "Assembly ID", 
                 `Assembly Name` = "Assembly Name",
                 `Isolation Date` = "Isolation Date", Host = "Host", 
                 Country = "Country", City = "City")
    
    if(!is.null(Vis$meta_nj) && ncol(Vis$meta_nj) > 11) {
      choices <- append(choices, names(Vis$meta_nj)[14:ncol(Vis$meta_nj)])
    }
    
    output <- render_plot_control(input_id = "nj_tiplab",
                                  input_type = "selectInput",
                                  choices = choices, 
                                  reactive_value = nj_tiplab_val(),
                                  default_value = "Assembly Name",
                                  reset = isolate(Vis$nj_tiplab_val_reset))
    
    isolate(Vis$nj_tiplab_val_reset <- FALSE)
    
    output
  })
  
  output$nj_align_ui <- renderUI({
    output <- render_plot_control(
      input_id = "nj_align",
      input_type = "materialSwitch",
      label = h5(
        p("Align"), 
        style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
      reactive_value = nj_align_val(),
      default_value = FALSE,
      div_class = "mat-switch-align",
      reset = isolate(Vis$nj_align_reset),
      right = TRUE,
      show_condition = !is.null(Vis$tree_algo) && Vis$tree_algo == "NJ")
    
    isolate(Vis$nj_align_reset <- FALSE)
    
    output
  })
  
  output$nj_tiplab_angle_ui <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiplab_angle",
      input_type = "sliderInput",
      label = h5("Angle", style = "color:white; margin-bottom: 0px"),
      min = -90,
      max = 90,
      width = "150px",
      reactive_value = nj_tiplab_angle_val(),
      default_value = 0,
      reset = isolate(Vis$nj_tiplab_angle_reset),
      right = TRUE,
      show_condition = nj_layout_val() != "inward" & 
        nj_layout_val() != "circular")
    
    isolate(Vis$nj_tiplab_angle_reset <- FALSE)
    
    output
  })
  
  # Branch label
  output$nj_branch_label <- renderUI({
    output <- render_plot_control(
      input_id = "nj_branch_label",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      reactive_value = nj_branch_label_val(),
      default_value = "Host",
      reset = isolate(Vis$nj_branch_label_val_reset))
    
    isolate(Vis$nj_branch_label_val_reset <- FALSE)
    
    output
  })
  
  # Custom label
  output$nj_custom_label_select <- renderUI({
    if(!is.null(Vis$custom_label_nj)) {
      if(nrow(Vis$custom_label_nj) > 0) {
        choices <- Vis$custom_label_nj[,1]
      } else {
        choices <- NULL
      }
    } else{
      choices <- NULL
    }
    
    div(
      class = "nj-custom-labe-sel",
      selectInput(
        "nj_custom_label_sel",
        "",
        choices = choices
      )
    )
  })
  
  output$nj_custom_labelsize <- renderUI({
    if(length(Vis$custom_label_nj) > 0) {
      if(!is.null(Vis$nj_label_size[[input$nj_custom_label_sel]])) {
        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
                    label = "",
                    min = 0, max = 10, step = 0.5, ticks = F,
                    value = Vis$nj_label_size[[input$nj_custom_label_sel]],
                    width = "150px")
      } else {
        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
                    label = "",
                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
                    width = "150px")
      }
    } else {
      sliderInput(inputId = paste0("nj_slider_size"),
                  label = "",
                  min = 0, max = 10, step = 0.5, ticks = F, value = 5,
                  width = "150px")
    } 
  })
  
  output$nj_sliderInput_y <- renderUI({
    if(!is.null(Vis$custom_label_nj)) {
      if(length(Vis$custom_label_nj) > 0) {
        
        inputId <- paste0("nj_slider_", input$nj_custom_label_sel, "_y")
        max <- sum(DB$data$Include)
        
        if(!is.null(Vis$nj_label_pos_y[[input$nj_custom_label_sel]])) {
          value <- Vis$nj_label_pos_y[[input$nj_custom_label_sel]]
        } else {
          value <- round(sum(DB$data$Include) / 2, 0)
        }
      } else {
        inputId <- "nj_slider_y"
        max <- 10
        value <- 5
      }
    } else {
      inputId <- "nj_slider_y"
      max <- 10
      value <- 5
    }
    
    sliderInput(inputId = inputId,
                label = "",
                min = 0, 
                max = max, 
                value = value,
                width = "150px",
                ticks = FALSE)
  })
  
  output$nj_sliderInput_x <- renderUI({
    if(!is.null(Vis$custom_label_nj)) {
      if(length(Vis$custom_label_nj) > 0) {
        inputId <- paste0("nj_slider_", input$nj_custom_label_sel, "_x")
        
        if(!is.null(Vis$nj_label_pos_x[[input$nj_custom_label_sel]])) {
          max <- 50
          value <- Vis$nj_label_pos_x[[input$nj_custom_label_sel]]
        } else {
          if(!is.null(Vis$nj_max_x)) {
            max <- round(Vis$nj_max_x, 0)
            value <- round(Vis$nj_max_x / 2, 0)
          } else {
            max <- 10
            value <- 1
          }
        }
      } else {
        inputId <- "nj_slider_x"
        max <- 10
        value <- 5
      } 
    } else {
      inputId <- "nj_slider_x"
      max <- 10
      value <- 5
    }
    
    sliderInput(inputId = inputId,
                label = "",
                min = 0, 
                max = max, 
                value = value,
                step = 1, 
                ticks = FALSE,
                width = "100%")
  })
  
  ##### Variable Menu ----
  
  ###### Variable Control Values ----
  
  # Tip label mapping
  nj_mapping_show_val <- reactiveVal()
  nj_color_mapping_reactive <- reactive({
    ifelse(!is.null(input$nj_color_mapping),
           input$nj_color_mapping,
           "Country")}) |> debounce(100)
  nj_color_mapping_val <- reactiveVal()
  nj_tiplab_scale_reactive <- reactive({
    ifelse(
      !is.null(input$nj_tiplab_scale),
      input$nj_tiplab_scale,
      nj_tiplab_scale_val_default())
  }) |> debounce(100)
  nj_tiplab_scale_val <- reactiveVal()
  nj_color_mapping_div_mid_reactive <- reactive({
    ifelse(!is.null(input$nj_color_mapping_div_mid),
           input$nj_color_mapping_div_mid,
           "Mean")}) |> debounce(100)
  nj_color_mapping_div_mid_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_mapping_show),
           nj_mapping_show_val(input$nj_mapping_show),
           nj_mapping_show_val(FALSE))
    
    nj_color_mapping_val(nj_color_mapping_reactive())
    
    nj_tiplab_scale_val(nj_tiplab_scale_reactive())
    
    nj_color_mapping_div_mid_val(nj_color_mapping_div_mid_reactive())
  })
  
  # Tip points mapping
  nj_tipcolor_mapping_show_val <- reactiveVal()
  nj_tipcolor_mapping_reactive <- reactive({
    ifelse(!is.null(input$nj_tipcolor_mapping),
           input$nj_tipcolor_mapping,
           "Country")}) |> debounce(100)
  nj_tipcolor_mapping_val <- reactiveVal()
  nj_tippoint_scale_reactive <- reactive({
    ifelse(!is.null(input$nj_tippoint_scale),
           input$nj_tippoint_scale,
           nj_tippoint_scale_val_default())}) |> debounce(100)
  nj_tippoint_scale_val <- reactiveVal()
  nj_tipcolor_mapping_div_mid_reactive <- reactive({
    ifelse(!is.null(input$nj_tipcolor_mapping_div_mid),
           input$nj_tipcolor_mapping_div_mid,
           "Mean")
  })
  nj_tipcolor_mapping_div_mid_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_tipcolor_mapping_show),
           nj_tipcolor_mapping_show_val(input$nj_tipcolor_mapping_show),
           nj_tipcolor_mapping_show_val(FALSE))
    
    nj_tipcolor_mapping_val(nj_tipcolor_mapping_reactive())
    
    nj_tippoint_scale_val(nj_tippoint_scale_reactive())
    
    nj_tipcolor_mapping_div_mid_val(nj_tipcolor_mapping_div_mid_reactive())
  })
  
  # Tip shape mapping
  nj_tipshape_mapping_show_val <- reactiveVal()
  nj_tipshape_mapping_reactive <- reactive({
    ifelse(!is.null(input$nj_tipshape_mapping),
           input$nj_tipshape_mapping,
           "Host")}) |> debounce(100)
  nj_tipshape_mapping_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_tipshape_mapping_show),
           nj_tipshape_mapping_show_val(input$nj_tipshape_mapping_show),
           nj_tipshape_mapping_show_val(FALSE))
    
    nj_tipshape_mapping_val(nj_tipshape_mapping_reactive())
  })
  
  # Tiles mapping
  nj_tiles_show_1_val <- reactiveVal()
  nj_tiles_show_2_val <- reactiveVal()
  nj_tiles_show_3_val <- reactiveVal()
  nj_tiles_show_4_val <- reactiveVal()
  nj_tiles_show_5_val <- reactiveVal()
  nj_fruit_variable_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_variable),
           input$nj_fruit_variable,
           "Isolation Date")}) |> debounce(100)
  nj_fruit_variable_val <- reactiveVal()
  nj_fruit_variable_2_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_variable_2),
           input$nj_fruit_variable_2,
           "Isolation Date")}) |> debounce(100)
  nj_fruit_variable_2_val <- reactiveVal()
  nj_fruit_variable_3_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_variable_3),
           input$nj_fruit_variable_3,
           "Isolation Date")}) |> debounce(100)
  nj_fruit_variable_3_val <- reactiveVal()
  nj_fruit_variable_4_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_variable_4),
           input$nj_fruit_variable_4,
           "Isolation Date")}) |> debounce(100)
  nj_fruit_variable_4_val <- reactiveVal()
  nj_fruit_variable_5_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_variable_5),
           input$nj_fruit_variable_5,
           "Isolation Date")}) |> debounce(100)
  nj_fruit_variable_5_val <- reactiveVal()
  nj_tiles_scale_1_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_scale_1),
           input$nj_tiles_scale_1,
           nj_tiles_scale_1_val_default())}) |> debounce(100)
  nj_tiles_scale_1_val <- reactiveVal()
  nj_tiles_scale_2_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_scale_2),
           input$nj_tiles_scale_2,
           nj_tiles_scale_2_val_default())}) |> debounce(100)
  nj_tiles_scale_2_val <- reactiveVal()
  nj_tiles_scale_3_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_scale_3),
           input$nj_tiles_scale_3,
           nj_tiles_scale_3_val_default())}) |> debounce(100)
  nj_tiles_scale_3_val <- reactiveVal()
  nj_tiles_scale_4_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_scale_4),
           input$nj_tiles_scale_4,
           nj_tiles_scale_4_val_default())}) |> debounce(100)
  nj_tiles_scale_4_val <- reactiveVal()
  nj_tiles_scale_5_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_scale_5),
           input$nj_tiles_scale_5,
           nj_tiles_scale_5_val_default())}) |> debounce(100)
  nj_tiles_scale_5_val <- reactiveVal()
  nj_tiles_mapping_div_mid_1_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_mapping_div_mid_1),
           input$nj_tiles_mapping_div_mid_1,
           "Mean")}) |> debounce(100)
  nj_tiles_mapping_div_mid_1_val <- reactiveVal()
  nj_tiles_mapping_div_mid_2_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_mapping_div_mid_2),
           input$nj_tiles_mapping_div_mid_2,
           "Mean")}) |> debounce(100)
  nj_tiles_mapping_div_mid_2_val <- reactiveVal()
  nj_tiles_mapping_div_mid_3_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_mapping_div_mid_3),
           input$nj_tiles_mapping_div_mid_3,
           "Mean")}) |> debounce(100)
  nj_tiles_mapping_div_mid_3_val <- reactiveVal()
  nj_tiles_mapping_div_mid_4_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_mapping_div_mid_4),
           input$nj_tiles_mapping_div_mid_4,
           "Mean")}) |> debounce(100)
  nj_tiles_mapping_div_mid_4_val <- reactiveVal()
  nj_tiles_mapping_div_mid_5_reactive <- reactive({
    ifelse(!is.null(input$nj_tiles_mapping_div_mid_5),
           input$nj_tiles_mapping_div_mid_5,
           "Mean")}) |> debounce(100)
  nj_tiles_mapping_div_mid_5_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_tiles_show_1),
           nj_tiles_show_1_val(input$nj_tiles_show_1),
           nj_tiles_show_1_val(FALSE))
    
    ifelse(!is.null(input$nj_tiles_show_2),
           nj_tiles_show_2_val(input$nj_tiles_show_2),
           nj_tiles_show_2_val(FALSE))
    
    ifelse(!is.null(input$nj_tiles_show_3),
           nj_tiles_show_3_val(input$nj_tiles_show_3),
           nj_tiles_show_3_val(FALSE))
    
    ifelse(!is.null(input$nj_tiles_show_4),
           nj_tiles_show_4_val(input$nj_tiles_show_4),
           nj_tiles_show_4_val(FALSE))
    
    ifelse(!is.null(input$nj_tiles_show_5),
           nj_tiles_show_5_val(input$nj_tiles_show_5),
           nj_tiles_show_5_val(FALSE))
    
    nj_fruit_variable_val(nj_fruit_variable_reactive())
    nj_fruit_variable_2_val(nj_fruit_variable_2_reactive())
    nj_fruit_variable_3_val(nj_fruit_variable_3_reactive())
    nj_fruit_variable_4_val(nj_fruit_variable_4_reactive())
    nj_fruit_variable_5_val(nj_fruit_variable_5_reactive())
    
    nj_tiles_scale_1_val(nj_tiles_scale_1_reactive())
    nj_tiles_scale_2_val(nj_tiles_scale_2_reactive())
    nj_tiles_scale_3_val(nj_tiles_scale_3_reactive())
    nj_tiles_scale_4_val(nj_tiles_scale_4_reactive())
    nj_tiles_scale_5_val(nj_tiles_scale_5_reactive())
    
    nj_tiles_mapping_div_mid_1_val(nj_tiles_mapping_div_mid_1_reactive())
    nj_tiles_mapping_div_mid_2_val(nj_tiles_mapping_div_mid_2_reactive())
    nj_tiles_mapping_div_mid_3_val(nj_tiles_mapping_div_mid_3_reactive())
    nj_tiles_mapping_div_mid_4_val(nj_tiles_mapping_div_mid_4_reactive())
    nj_tiles_mapping_div_mid_5_val(nj_tiles_mapping_div_mid_5_reactive())
  })
  
  # Heatmap mapping
  nj_heatmap_show_val <- reactiveVal()
  nj_heatmap_select_val <- reactiveVal()
  nj_heatmap_scale_val <- reactiveVal()
  nj_heatmap_div_mid_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_heatmap_show),
           nj_heatmap_show_val(input$nj_heatmap_show),
           nj_heatmap_show_val(FALSE))
    
    nj_heatmap_select_val(input$nj_heatmap_select)
    
    ifelse(!is.null(input$nj_heatmap_scale),
           nj_heatmap_scale_val(input$nj_heatmap_scale),
           nj_heatmap_scale_val(nj_heatmap_scale_val_default()))
    
    ifelse(!is.null(input$nj_heatmap_div_mid),
           nj_heatmap_div_mid_val(input$nj_heatmap_div_mid),
           nj_heatmap_div_mid_val("Mean"))
  })
  
  ###### Variable Interface ----
  
  observeEvent(input$nj_variable_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_variable_menu")
    
    output$tree_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Variable Mapping",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    align = "left",
                    h4(p("Tip Label Color"), style = "color:white; position: relative; right: -15px; ")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_mapping_show",
                        "",
                        value = isolate(nj_mapping_show_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  uiOutput("nj_color_mapping")
                ),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    actionBttn(
                      "nj_variable_tiplab_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        uiOutput("nj_tiplab_scale"),
                        br(),
                        uiOutput("nj_tiplab_mid_scale")
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  uiOutput("nj_tiplab_mapping_info")
                )
              ),
              hr(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    align = "left",
                    h4(p("Tip Point Color"), style = "color:white; position: relative; right: -15px; ")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tipcolor_mapping_show",
                        "",
                        value = isolate(nj_tipcolor_mapping_show_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  uiOutput("nj_tipcolor_mapping")
                ),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    actionBttn(
                      "nj_variable_tipcolor_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        uiOutput("nj_tippoint_scale"),
                        br(),
                        uiOutput("nj_tippoint_mid_scale")
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  uiOutput("nj_tipcolor_mapping_info")
                )
              ),
              hr(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    align = "left",
                    h4(p("Tip Point Shape"), style = "color:white; position: relative; right: -15px; ")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tipshape_mapping_show",
                        "",
                        value = isolate(nj_tipshape_mapping_show_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  uiOutput("nj_tipshape_mapping")
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  uiOutput("nj_tipshape_mapping_info")
                )
              ),
              hr(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    align = "left",
                    h4(p("Tiles"), style = "color:white; position: relative; right: -15px; ")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    div(
                      class = "tile-sel",
                      selectInput(
                        "nj_tile_num",
                        "",
                        choices = 1:5,
                        width = "50px"
                      )
                    )
                  )
                ),
                column(
                  width = 4,
                  align = "center",
                  conditionalPanel(
                    "input.nj_tile_num == 1",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tiles_show_1",
                        "",
                        value = isolate(nj_tiles_show_1_val())
                      )
                    )
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 2",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tiles_show_2",
                        "",
                        value = isolate(nj_tiles_show_2_val())
                      )
                    )
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 3",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tiles_show_3",
                        "",
                        value = isolate(nj_tiles_show_3_val())
                      )
                    )
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 4",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tiles_show_4",
                        "",
                        value = isolate(nj_tiles_show_4_val())
                      )
                    )
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 5",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tiles_show_5",
                        "",
                        value = isolate(nj_tiles_show_5_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  conditionalPanel(
                    "input.nj_tile_num == 1",
                    uiOutput("nj_fruit_variable")
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 2",
                    uiOutput("nj_fruit_variable_2")
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 3",
                    uiOutput("nj_fruit_variable_3")
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 4",
                    uiOutput("nj_fruit_variable_4")
                  ),
                  conditionalPanel(
                    "input.nj_tile_num == 5",
                    uiOutput("nj_fruit_variable_5")
                  )
                ),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    actionBttn(
                      "nj_variable_tiles_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        conditionalPanel(
                          "input.nj_tile_num == 1",
                          uiOutput("nj_tiles_scale_1"),
                          br(),
                          uiOutput("nj_tiles_mid_scale_1")
                        ),
                        conditionalPanel(
                          "input.nj_tile_num == 2",
                          uiOutput("nj_tiles_scale_2"),
                          br(),
                          uiOutput("nj_tiles_mid_scale_2")
                        ),
                        conditionalPanel(
                          "input.nj_tile_num == 3",
                          uiOutput("nj_tiles_scale_3"),
                          br(),
                          uiOutput("nj_tiles_mid_scale_3")
                        ),
                        conditionalPanel(
                          "input.nj_tile_num == 4",
                          uiOutput("nj_tiles_scale_4"),
                          br(),
                          uiOutput("nj_tiles_mid_scale_4")
                        ),
                        conditionalPanel(
                          "input.nj_tile_num == 5",
                          uiOutput("nj_tiles_scale_5"),
                          br(),
                          uiOutput("nj_tiles_mid_scale_5")
                        )
                      )
                    )
                  )
                )
              ), 
              fluidRow(
                column(
                  width = 12,
                  uiOutput("nj_fruit_mapping_info")
                )
              ),
              hr(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    align = "left",
                    h4(p("Heatmap"), style = "color:grey; position: relative; right: -15px; ")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      shinyjs::disabled(
                        materialSwitch(
                          "nj_heatmap_show",
                          "",
                          value = isolate(nj_heatmap_show_val())
                        )
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  shinyjs::disabled(
                    actionButton("nj_heatmap_button", "Select Variables")
                  )
                ),
                column(1),
                column(
                  width = 3,
                  align = "center",
                  dropMenu(
                    shinyjs::disabled(
                      actionBttn(
                        "nj_variable_heatmap_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      )
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        uiOutput("nj_heatmap_scale"),
                        br(),
                        uiOutput("nj_heatmap_mid_scale")
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  uiOutput("nj_heatmap_mapping_info")
                )
              ),
              br()
            )
          )
        )
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ###### Variable Inputs ----
  
  # Tip label variable mapping
  
  output$nj_color_mapping <- renderUI({
    output <- render_plot_control(
      input_id = "nj_color_mapping",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      reactive_value = nj_color_mapping_val(),
      default_value = "Country",
      reset = isolate(Vis$nj_color_mapping_val_reset),
      show_condition = isTRUE(nj_mapping_show_val()))
    
    isolate(Vis$nj_color_mapping_val_reset <- FALSE)
    
    output
  })
  
  output$nj_tiplab_scale <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiplab_scale",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_color_mapping_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiplab_scale_val(),
      default_value = nj_tiplab_scale_val_default(),
      reset = isolate(Vis$nj_tiplab_scale_reset),
      show_condition = nj_mapping_show_val())
    
    isolate(Vis$nj_tiplab_scale_val_reset <- FALSE)
    
    output
  })
  
  output$nj_tiplab_mid_scale <- renderUI({
    output <- render_plot_control(
      input_id = "nj_color_mapping_div_mid",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_color_mapping_div_mid_val(),
      default_value = "Mean",
      reset = isolate(Vis$nj_color_mapping_div_mid_reset),
      show_condition = isTRUE(nj_mapping_show_val()) &&
        !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_color_mapping_val()])) &&
        nj_tiplab_scale_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_color_mapping_div_mid_reset <- FALSE)
    
    output
  })
  
  output$nj_tiplab_mapping_info <- renderUI({
    req(Vis$meta_nj)
    
    if(is.numeric(unlist(Vis$meta_nj[nj_color_mapping_val()]))) {
      fluidRow(
        h5("Continous values", 
           style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
      ) 
    } else {
      if(length(unique(unlist(Vis$meta_nj[nj_color_mapping_val()]))) > 7) {
        fluidRow(
          h5(paste0("> 7 (", 
                    length(unique(unlist(Vis$meta_nj[nj_color_mapping_val()]))),
                    ") categorical values"), 
             style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
        )
      } else {
        fluidRow(
          h5(paste0(length(unique(unlist(Vis$meta_nj[nj_color_mapping_val()]))), 
                    paste0(" categorical values")), 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
        )
      }
    }
  })
  
  # Tip point variable mapping
  
  output$nj_tipcolor_mapping <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tipcolor_mapping",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      reactive_value = nj_tipcolor_mapping_val(),
      default_value = "Country",
      reset = isolate(Vis$nj_tipcolor_mapping_val_reset),
      show_condition = isTRUE(nj_tipcolor_mapping_show_val()))
    
    isolate(Vis$nj_tipcolor_mapping_val_reset <- FALSE)
    
    output
  })
  
  output$nj_tippoint_scale <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tippoint_scale",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_tipcolor_mapping_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tippoint_scale_val(),
      default_value = nj_tippoint_scale_val_default(),
      reset = isolate(Vis$nj_tippoint_scale_reset),
      show_condition = nj_tipcolor_mapping_show_val())
    
    isolate(Vis$nj_tippoint_scale_reset <- FALSE)
    
    output
  })
  
  output$nj_tippoint_mid_scale <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tipcolor_mapping_div_mid",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tipcolor_mapping_div_mid_val(),
      default_value = "Mean",
      reset = isolate(Vis$nj_tipcolor_mapping_div_mid_reset),
      show_condition = isTRUE(nj_tipcolor_mapping_show_val()) && 
        !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_tipcolor_mapping_val()])) &&
        nj_tippoint_scale_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tipcolor_mapping_div_mid_reset <- FALSE)
    
    output
  })
  
  output$nj_tipcolor_mapping_info <- renderUI({
    req(Vis$meta_nj)
    
    if(is.numeric(unlist(Vis$meta_nj[nj_tipcolor_mapping_val()]))) {
      fluidRow(
        h5("Continous values", 
           style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
      ) 
    } else {
      if(length(unique(unlist(Vis$meta_nj[nj_tipcolor_mapping_val()]))) > 7) {
        fluidRow(
          h5(paste0("> 7 (", 
                    length(unique(unlist(Vis$meta_nj[nj_tipcolor_mapping_val()]))), 
                    ") categorical values"), 
             style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
        )
      } else {
        fluidRow(
          h5(paste0(length(unique(unlist(Vis$meta_nj[nj_tipcolor_mapping_val()]))), 
                    paste0(" categorical values")), 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")      
        )
      }
    }
  })
  
  # Tip shape variable mapping
  
  output$nj_tipshape_mapping <- renderUI({
    if(!is.null(Vis$meta_nj)) {
      if(ncol(Vis$meta_nj) == 11) {
        choices <- c( `Isolation Date` = "Isolation Date",
                      Host = "Host", Country = "Country", City = "City")
      } else {
        choices <- append(c(`Isolation Date` = "Isolation Date", 
                            Host = "Host", Country = "Country", City = "City"),
                          names(Vis$meta_nj)[14:ncol(Vis$meta_nj)])
        
        if(!is.null(DB$cust_var) && length(DB$cust_var) > 0 ) {
          cont_vars <- DB$cust_var$Variable[which(DB$cust_var$Type == "cont")]
          choices <- choices[-which(choices %in% cont_vars)]
        }
      }
    } else {
      choices = c(`Isolation Date` = "Isolation Date", Host = "Host",
                  Country = "Country", City = "City")
    }
    
    output <- render_plot_control(
      input_id = "nj_tipshape_mapping",
      input_type = "selectInput",
      choices = choices,
      reactive_value = nj_tipshape_mapping_val(),
      default_value = "Host",
      reset = isolate(Vis$nj_tipshape_mapping_val_reset),
      show_condition = isTRUE(nj_tipshape_mapping_show_val()))
    
    isolate(Vis$nj_tipshape_mapping_val_reset <- FALSE)
    
    output
  })
  
  output$nj_tipshape_mapping_info <- renderUI({
    req(Vis$meta_nj)
    
    if(is.numeric(unlist(Vis$meta_nj[nj_tipshape_mapping_val()]))) {
      fluidRow(
        h5("Mapping continous variables to shape not possible", 
           style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
      )
    } else {
      if(length(unique(unlist(Vis$meta_nj[nj_tipshape_mapping_val()]))) > 6) {
        fluidRow(
          h5("Mapping > 6 variables to shape not possible", 
             style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
        )
      } else {
        fluidRow(
          h5(paste0(length(unique(unlist(Vis$meta_nj[nj_tipshape_mapping_val()]))), 
                    paste0(" categorical values")), 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
        )    
      }
    }
  })
  
  # Tiles variables mapping
  
  output$nj_fruit_variable <- renderUI({
    output <- render_plot_control(
      input_id = "nj_fruit_variable",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      div_class = "nj-fruit-variable",
      reactive_value = nj_fruit_variable_val(),
      default_value = "Isolation Date",
      reset = isolate(Vis$nj_fruit_variable_val_reset),
      show_condition = isTRUE(nj_tiles_show_1_val()))
    
    isolate(Vis$nj_fruit_variable_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_variable_2 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_fruit_variable_2",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      div_class = "nj-fruit-variable",
      reactive_value = nj_fruit_variable_2_val(),
      default_value = "Isolation Date",
      reset = isolate(Vis$nj_fruit_variable_2_val_reset),
      show_condition = isTRUE(nj_tiles_show_2_val()))
    
    isolate(Vis$nj_fruit_variable_2_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_variable_3 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_fruit_variable_3",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      div_class = "nj-fruit-variable",
      reactive_value = nj_fruit_variable_3_val(),
      default_value = "Isolation Date",
      reset = isolate(Vis$nj_fruit_variable_3_val_reset),
      show_condition = isTRUE(nj_tiles_show_3_val()))
    
    isolate(Vis$nj_fruit_variable_3_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_variable_4 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_fruit_variable_4",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      div_class = "nj-fruit-variable",
      reactive_value = nj_fruit_variable_4_val(),
      default_value = "Isolation Date",
      reset = isolate(Vis$nj_fruit_variable_4_val_reset),
      show_condition = isTRUE(nj_tiles_show_4_val()))
    
    isolate(Vis$nj_fruit_variable_4_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_variable_5 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_fruit_variable_5",
      input_type = "selectInput",
      choices = determine_variable_choices(Vis$meta_nj),
      div_class = "nj-fruit-variable",
      reactive_value = nj_fruit_variable_5_val(),
      default_value = "Isolation Date",
      reset = isolate(Vis$nj_fruit_variable_5_val_reset),
      show_condition = isTRUE(nj_tiles_show_5_val()))
    
    isolate(Vis$nj_fruit_variable_5_val_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_scale_1 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_scale_1",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj, 
                                        variable_val = nj_fruit_variable_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiles_scale_1_val(),
      default_value = nj_tiles_scale_1_val_default(),
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_scale_1_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_tiles_show_1_val())
    
    isolate(Vis$nj_tiles_scale_1_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_scale_2 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_scale_2",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_fruit_variable_2_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiles_scale_2_val(),
      default_value = nj_tiles_scale_2_val_default(),
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_scale_2_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_tiles_show_2_val())
    
    isolate(Vis$nj_tiles_scale_2_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_scale_3 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_scale_3",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_fruit_variable_3_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiles_scale_3_val(),
      default_value = nj_tiles_scale_3_val_default(),
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_scale_3_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_tiles_show_3_val())
    
    isolate(Vis$nj_tiles_scale_3_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_scale_4 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_scale_4",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_fruit_variable_4_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiles_scale_4_val(),
      default_value = nj_tiles_scale_4_val_default(),
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_scale_4_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_tiles_show_4_val())
    
    isolate(Vis$nj_tiles_scale_4_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_scale_5 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_scale_5",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = determine_scale_choices(meta_nj = Vis$meta_nj,
                                        variable_val = nj_fruit_variable_5_val(),
                                        gradient_scales = gradient_scales, 
                                        diverging_scales = diverging_scales, 
                                        qualitative_scales = qualitative_scales, 
                                        sequential_scales = sequential_scales),
      reactive_value = nj_tiles_scale_5_val(),
      default_value = nj_tiles_scale_5_val_default(),
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_scale_5_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_tiles_show_5_val())
    
    isolate(Vis$nj_tiles_scale_5_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_mid_scale_1 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_mapping_div_mid_1",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tiles_mapping_div_mid_1_val(),
      default_value = "Mean",
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_mapping_div_mid_1_reset),
      show_condition = nj_tiles_show_1_val() && !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_val()])) &&
        nj_tiles_scale_1_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tiles_mapping_div_mid_1_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_mid_scale_2 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_mapping_div_mid_2",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tiles_mapping_div_mid_2_val(),
      default_value = "Mean",
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_mapping_div_mid_2_reset),
      show_condition = nj_tiles_show_2_val() && !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_2_val()])) &&
        nj_tiles_scale_2_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tiles_mapping_div_mid_2_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_mid_scale_3 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_mapping_div_mid_3",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tiles_mapping_div_mid_3_val(),
      default_value = "Mean",
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_mapping_div_mid_3_reset),
      show_condition = nj_tiles_show_3_val() && !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_3_val()])) &&
        nj_tiles_scale_3_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tiles_mapping_div_mid_3_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_mid_scale_4 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_mapping_div_mid_4",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tiles_mapping_div_mid_4_val(),
      default_value = "Mean",
      div_class = "nj-tiles-scale",
      reset = isolate(Vis$nj_tiles_mapping_div_mid_4_reset),
      show_condition = nj_tiles_show_4_val() && !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_4_val()])) &&
        nj_tiles_scale_4_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tiles_mapping_div_mid_4_reset <- FALSE)
    
    output
  })
  
  output$nj_tiles_mid_scale_5 <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tiles_mapping_div_mid_5",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_tiles_mapping_div_mid_5_val(),
      default_value = "Mean",
      reset = isolate(Vis$nj_tiles_mapping_div_mid_5_reset),
      show_condition = nj_tiles_show_5_val() && !is.null(Vis$meta_nj) &&
        is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_5_val()])) &&
        nj_tiles_scale_5_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_tiles_mapping_div_mid_5_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_mapping_info <- renderUI({
    req(input$nj_tile_num, Vis$meta_nj)
    
    if(input$nj_tile_num == 1) {
      
      if(is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_val()]))) {
        fluidRow(
          h5("Continous values", 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
        ) 
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_val()]))) > 7) {
          fluidRow(
            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[nj_fruit_variable_val()]))), 
                      ") categorical values"), 
               style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        } else {
          fluidRow(
            h5(paste0(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_val()]))), 
                      paste0(" categorical values")), 
               style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        }
      }
    } else if (input$nj_tile_num == 2) {
      
      if(is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_2_val()]))) {
        fluidRow(
          h5("Continous values", 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
        )
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_2_val()]))) > 7) {
          fluidRow(
            h5(paste0("> 7 (", 
                      length(unique(unlist(Vis$meta_nj[nj_fruit_variable_2_val()]))), 
                      ") categorical values"), 
               style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        } else {
          fluidRow(
            h5(paste0(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_2_val()]))), 
                      paste0(" categorical values")), 
               style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        }
      }
    } else if (input$nj_tile_num == 3) {
      if(is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_3_val()]))) {
        fluidRow(
          h5("Continous values", 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
        )
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_3_val()]))) > 7) {
          fluidRow(
            h5(paste0("> 7 (", 
                      length(unique(unlist(Vis$meta_nj[nj_fruit_variable_3_val()]))), 
                      ") categorical values"), 
               style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        } else {
          fluidRow(
            h5(paste0(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_3_val()]))), 
                      paste0(" categorical values")), 
               style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        }
      }
    } else if (input$nj_tile_num == 4) {
      if(is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_4_val()]))) {
        fluidRow(
          h5("Continous values", 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
        )
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_4_val()]))) > 7) {
          fluidRow(
            h5(paste0("> 7 (", 
                      length(unique(unlist(Vis$meta_nj[nj_fruit_variable_4_val()]))), 
                      ") categorical values"), 
               style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        } else {
          fluidRow(
            h5(paste0(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_4_val()]))), 
                      paste0(" categorical values")), 
               style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        }
      }
    } else if (input$nj_tile_num == 5) {
      if(is.numeric(unlist(Vis$meta_nj[nj_fruit_variable_5_val()]))) {
        fluidRow(
          h5("Continous values", 
             style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")
        )
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_5_val()]))) > 7) {
          fluidRow(
            h5(paste0("> 7 (", 
                      length(unique(unlist(Vis$meta_nj[nj_fruit_variable_5_val()]))), 
                      ") categorical values"), 
               style = "color: #E18B00; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        } else {
          fluidRow(
            h5(paste0(length(unique(unlist(Vis$meta_nj[nj_fruit_variable_5_val()]))), 
                      paste0(" categorical values")), style = "color: white; font-size: 12px; margin-top: 5px; margin-left: 35px; margin-bottom: -12px;")        
          )
        }
      }
    }
  })
  
  # Heatmap variables mapping
  
  output$nj_heatmap_sel <- renderUI({
    
    no_screened <- FALSE
    
    if(!is.null(Vis$meta_nj)) {
      
      meta <- select(Vis$meta_nj, -c(taxa, Index, `Assembly ID`, 
                                     `Assembly Name`, Scheme, `Typing Date`, 
                                     Successes, Errors, Screened))
      
      if(input$nj_heatmap_map == "Variables") {
        meta <- select(meta, -colnames(Vis$amr_nj))
        
        # Identify numeric columns
        numeric_columns <- sapply(meta, is.numeric)
        numeric_column_names <- names(meta[numeric_columns])
        non_numeric_column_names <- names(meta)[!numeric_columns]
        non_numeric_column_names <- non_numeric_column_names[!numeric_columns]
        
        choices <- list()
        
        # Add Continuous list only if there are numeric columns
        if (length(numeric_column_names) > 0) {
          choices$Continuous <- as.list(setNames(numeric_column_names, 
                                                 numeric_column_names))
        }
        
        # Add Diverging list
        choices$Categorical <- setNames(non_numeric_column_names, 
                                        non_numeric_column_names)
      } else if(input$nj_heatmap_map == "AMR Profile") {
        if(!isTRUE(Screening$available) | sum(Vis$meta_nj$Screened == "Yes") == 0) {
          choices <- NULL
          no_screened <- TRUE
        } else {
          choices <- as.list(colnames(Vis$amr_nj))
        }
      }
    } else {
      if(input$nj_heatmap_map == "AMR Profile") {
        choices <- NULL
        if(!isTRUE(Screening$available)) {
          no_screened <- TRUE
        }
      }
      choices <- c(`Isolation Date` = "Isolation Date", Host = "Host", 
                   Country = "Country", City = "City")
    }
    
    output <- render_plot_control(
      input_id = "nj_heatmap_select",
      input_type = "pickerInput",
      multiple = TRUE,
      choices = choices,
      options = list(`live-search` = TRUE, `actions-box` = TRUE, size = 10, 
                     style = "background-color: white; border-radius: 5px;"),
      reactive_value = nj_heatmap_select_val(),
      default_value = NULL,
      reset = isolate(Vis$nj_heatmap_select_val_reset),
      show_condition = isFALSE(no_screened))
    
    isolate(Vis$nj_heatmap_select_val_reset <- FALSE)
    
    output
  })
  
  output$nj_heatmap_scale <- renderUI({
    
    if(!is.null(Vis$meta_nj)) {
      if(class(unlist(Vis$meta_nj[nj_heatmap_select_val()])) == "numeric") {
        choices <- list(Continous = gradient_scales,
                        Diverging = diverging_scales)
      } else {
        if(length(unique(unlist(Vis$meta_nj[nj_heatmap_select_val()]))) > 7) {
          choices <- list(Gradient = gradient_scales)
        } else {
          choices <- list(Qualitative = qualitative_scales,
                          Sequential = sequential_scales)
        }
      }
    } else {
      choices <- list(Qualitative = qualitative_scales,
                      Sequential = sequential_scales)
    }
    
    output <- render_plot_control(
      input_id = "nj_heatmap_scale",
      input_type = "selectInput",
      label = h5("Color Scale", style = "color: white; margin-bottom: 0px;"),
      width = "150px",
      choices = choices,
      reactive_value = nj_heatmap_scale_val(),
      default_value = nj_heatmap_scale_val_default(),
      div_class = "nj-heatmap-scale",
      reset = isolate(Vis$nj_heatmap_scale_reset),
      show_condition = !is.null(Vis$meta_nj) && nj_heatmap_show_val())
    
    isolate(Vis$nj_heatmap_scale_reset <- FALSE)
    
    output
  })
  
  output$nj_heatmap_mid_scale <- renderUI({
    output <- render_plot_control(
      input_id = "nj_heatmap_div_mid",
      input_type = "selectInput",
      label = h5("Midpoint", style = "color: white; margin-bottom: 0px;"),
      choices = c("Zero", "Mean", "Median"),
      reactive_value = nj_heatmap_div_mid_val(),
      default_value = "Mean",
      div_class = "nj-heatmap-div-mid",
      reset = isolate(Vis$nj_heatmap_div_mid_val_reset),
      show_condition = isTRUE(nj_heatmap_show_val()) &&
        !is.null(Vis$meta_nj) &&
        any(sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric)) &&
        nj_heatmap_scale_val() %in% unlist(diverging_scales))
    
    isolate(Vis$nj_heatmap_div_mid_val_reset <- FALSE)
    
    output
  })
  
  output$nj_heatmap_mapping_info <- renderUI({
    req(Vis$meta_nj)
    
    if(!is.null(nj_heatmap_select_val())) {
      if(!(any(sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric)) & 
           any(!sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric)))) {
        if(any(sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric))) {
          fluidRow(
            h5("Continous values", 
               style = "color: white; font-size: 12px; margin-top: 10px; margin-left: 35px; margin-bottom: -12px;")
          ) 
        } else {
          if(length(unique(unlist(Vis$meta_nj[nj_heatmap_select_val()]))) > 7) {
            fluidRow(
              h5(paste0("> 7 categorical values"), 
                 style = "color: #E18B00; font-size: 12px; margin-top: 10px; margin-left: 35px; margin-bottom: -12px;")        
            )
          } else {
            fluidRow(
              h5("Categorical values", style = "color: white; font-size: 12px; margin-top: 10px; margin-left: 35px; margin-bottom: -12px;")        
            )
          }
        }
      } else {NULL}
    } else {NULL}
  })
  
  output$nj_heatmap_var_warning <- renderUI({
    if(!is.null(Vis$meta_nj) &&
       any(sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric)) & 
       any(!sapply(Vis$meta_nj[nj_heatmap_select_val()], is.numeric))) {
      h5("Heatmap with both categorical and continous values not possible", 
         style = "color: #E18B00; font-size: 12px; font-style: italic; margin-left: 20px")
    } else {h5("")}  
  })
  
  
  ##### Color Menu ----
  
  ###### Color Control Values ----
  
  nj_color_val <- reactiveVal()
  nj_bg_val <- reactiveVal()
  nj_title_color_val <- reactiveVal()
  nj_tiplab_color_val <- reactiveVal()
  nj_tiplab_fill_val <- reactiveVal()
  nj_branch_label_color_val <- reactiveVal()
  nj_tippoint_color_val <- reactiveVal()
  nj_nodepoint_color_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_color),
           nj_color_val(input$nj_color),
           nj_color_val("#000000"))
    
    ifelse(!is.null(input$nj_bg),
           nj_bg_val(input$nj_bg),
           nj_bg_val("#ffffff"))
    
    ifelse(!is.null(input$nj_title_color),
           nj_title_color_val(input$nj_title_color),
           nj_title_color_val("#000000"))
    
    ifelse(!is.null(input$nj_tiplab_color),
           nj_tiplab_color_val(input$nj_tiplab_color),
           nj_tiplab_color_val("#000000"))
    
    ifelse(!is.null(input$nj_tiplab_fill),
           nj_tiplab_fill_val(input$nj_tiplab_fill),
           nj_tiplab_fill_val("#84D9A0"))
    
    ifelse(!is.null(input$nj_branch_label_color),
           nj_branch_label_color_val(input$nj_branch_label_color),
           nj_branch_label_color_val("#FFB7B7"))
    
    ifelse(!is.null(input$nj_tippoint_color),
           nj_tippoint_color_val(input$nj_tippoint_color),
           nj_tippoint_color_val("#3A4657"))
    
    ifelse(!is.null(input$nj_nodepoint_color),
           nj_nodepoint_color_val(input$nj_nodepoint_color),
           nj_nodepoint_color_val("#3A4657"))
  })
  
  ###### Color Interface ----
  
  observeEvent(input$nj_color_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_color_menu")
    
    output$tree_controls <- renderUI(
      box(
        solidHeader = TRUE,
        status = "primary",
        width = "100%",
        title = "Color Menu",
        column(
          width = 12,
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Lines/Text')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_color",
                  selected = isolate(nj_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Background')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_bg",
                  selected = isolate(nj_bg_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Title')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_title_color",
                  selected = isolate(nj_title_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Tip Label')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_tiplab_color",
                  selected = isolate(nj_tiplab_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Label Panel')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_tiplab_fill",
                  selected = isolate(nj_tiplab_fill_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )  
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 13px; position: relative; top: 10px;', 
                            'Branch Label')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_branch_label_color",
                  selected = isolate(nj_branch_label_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Tip Point')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_tippoint_color",
                  selected = isolate(nj_tippoint_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Node Point')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              div(
                class = "control-color",
                colorPickr(
                  inputId = "nj_nodepoint_color",
                  selected = isolate(nj_nodepoint_color_val()),
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "100%"
                )
              )
            )
          ),
          br()
        )
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
    
  ##### Elements Menu ----
  
  ###### Elements Control Values ----
  
  # Tip points
  nj_tippoint_show_val <- reactiveVal()
  nj_tippoint_shape_reactive <- reactive({
    ifelse(!is.null(input$nj_tippoint_shape),
           input$nj_tippoint_shape,
           "circle")}) |> debounce(100)  
  nj_tippoint_shape_val <- reactiveVal()
  nj_tippoint_alpha_val <- reactiveVal()
  nj_tippoint_size_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_tippoint_show),
           nj_tippoint_show_val(input$nj_tippoint_show),
           nj_tippoint_show_val(FALSE))
    
    nj_tippoint_shape_val(nj_tippoint_shape_reactive())
    
    ifelse(!is.null(input$nj_tippoint_alpha),
           nj_tippoint_alpha_val(input$nj_tippoint_alpha),
           nj_tippoint_alpha_val(0.5))
    
    ifelse(!is.null(input$nj_tippoint_size),
           nj_tippoint_size_val(input$nj_tippoint_size),
           ifelse(!is.null(Vis$tippointsize_nj),
                  nj_tippoint_size_val(Vis$tippointsize_nj),
                  nj_tippoint_size_val(4)))
  })
  
  # Node points
  nj_nodepoint_show_val <- reactiveVal()
  nj_nodepoint_shape_val <- reactiveVal()
  nj_nodepoint_alpha_val <- reactiveVal()
  nj_nodepoint_size_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_nodepoint_show),
           nj_nodepoint_show_val(input$nj_nodepoint_show),
           nj_nodepoint_show_val(FALSE))
    
    ifelse(!is.null(input$nj_nodepoint_shape),
           nj_nodepoint_shape_val(input$nj_nodepoint_shape),
           nj_nodepoint_shape_val("circle"))
    
    ifelse(!is.null(input$nj_nodepoint_alpha),
           nj_nodepoint_alpha_val(input$nj_nodepoint_alpha),
           nj_nodepoint_alpha_val(1))
    
    ifelse(!is.null(input$nj_nodepoint_size),
           nj_nodepoint_size_val(input$nj_nodepoint_size),
           ifelse(!is.null(Vis$nodepointsize_nj),
                  nj_nodepoint_size_val(Vis$nodepointsize_nj),
                  nj_nodepoint_size_val(2.5)))
  })
  
  # Tiles
  nj_tile_number_val <- reactiveVal()
  nj_fruit_alpha_val <- reactiveVal()
  nj_fruit_alpha_2_val <- reactiveVal()
  nj_fruit_alpha_3_val <- reactiveVal()
  nj_fruit_alpha_4_val <- reactiveVal()
  nj_fruit_alpha_5_val <- reactiveVal()
  nj_fruit_width_circ_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_width_circ),
           input$nj_fruit_width_circ,
           fruit_width())}) |> debounce(100) 
  nj_fruit_width_circ_val <- reactiveVal()
  nj_fruit_width_circ_2_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_width_circ_2),
           input$nj_fruit_width_circ_2,
           fruit_width())}) |> debounce(100) 
  nj_fruit_width_circ_2_val <- reactiveVal()
  nj_fruit_width_circ_3_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_width_circ_3),
           input$nj_fruit_width_circ_3,
           fruit_width())}) |> debounce(100) 
  nj_fruit_width_circ_3_val <- reactiveVal()
  nj_fruit_width_circ_4_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_width_circ_4),
           input$nj_fruit_width_circ_4,
           fruit_width())}) |> debounce(100) 
  nj_fruit_width_circ_4_val <- reactiveVal()
  nj_fruit_width_circ_5_reactive <- reactive({
    ifelse(!is.null(input$nj_fruit_width_circ_5),
           input$nj_fruit_width_circ_5,
           fruit_width())}) |> debounce(100) 
  nj_fruit_width_circ_5_val <- reactiveVal()
  nj_fruit_offset_circ_val <- reactiveVal()
  nj_fruit_offset_circ_2_val <- reactiveVal()
  nj_fruit_offset_circ_3_val <- reactiveVal()
  nj_fruit_offset_circ_4_val <- reactiveVal()
  nj_fruit_offset_circ_5_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_tile_number),
           nj_tile_number_val(input$nj_tile_number),
           nj_tile_number_val(1))
    
    ifelse(!is.null(input$nj_fruit_alpha),
           nj_fruit_alpha_val(input$nj_fruit_alpha),
           nj_fruit_alpha_val(1))
    
    ifelse(!is.null(input$nj_fruit_alpha_2),
           nj_fruit_alpha_2_val(input$nj_fruit_alpha_2),
           nj_fruit_alpha_2_val(1))
    
    ifelse(!is.null(input$nj_fruit_alpha_3),
           nj_fruit_alpha_3_val(input$nj_fruit_alpha_3),
           nj_fruit_alpha_3_val(1))
    
    ifelse(!is.null(input$nj_fruit_alpha_4),
           nj_fruit_alpha_4_val(input$nj_fruit_alpha_4),
           nj_fruit_alpha_4_val(1))
    
    ifelse(!is.null(input$nj_fruit_alpha_5),
           nj_fruit_alpha_5_val(input$nj_fruit_alpha_5),
           nj_fruit_alpha_5_val(1))
    
    nj_fruit_width_circ_val(nj_fruit_width_circ_reactive())
    nj_fruit_width_circ_2_val(nj_fruit_width_circ_2_reactive())
    nj_fruit_width_circ_3_val(nj_fruit_width_circ_3_reactive())
    nj_fruit_width_circ_4_val(nj_fruit_width_circ_4_reactive())
    nj_fruit_width_circ_5_val(nj_fruit_width_circ_5_reactive())
    
    ifelse(!is.null(input$nj_fruit_offset_circ),
           nj_fruit_offset_circ_val(input$nj_fruit_offset_circ),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_fruit_offset_circ_val(0.15),
                  nj_fruit_offset_circ_val(0.05)))
    
    ifelse(!is.null(input$nj_fruit_offset_circ_2),
           nj_fruit_offset_circ_2_val(input$nj_fruit_offset_circ_2),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_fruit_offset_circ_2_val(0.15),
                  nj_fruit_offset_circ_2_val(0.05)))
    
    ifelse(!is.null(input$nj_fruit_offset_circ_3),
           nj_fruit_offset_circ_3_val(input$nj_fruit_offset_circ_3),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_fruit_offset_circ_3_val(0.15),
                  nj_fruit_offset_circ_3_val(0.05)))
    
    ifelse(!is.null(input$nj_fruit_offset_circ_4),
           nj_fruit_offset_circ_4_val(input$nj_fruit_offset_circ_4),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_fruit_offset_circ_4_val(0.15),
                  nj_fruit_offset_circ_4_val(0.05)))
    
    ifelse(!is.null(input$nj_fruit_offset_circ_5),
           nj_fruit_offset_circ_5_val(input$nj_fruit_offset_circ_5),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_fruit_offset_circ_5_val(0.15),
                  nj_fruit_offset_circ_5_val(0.05)))
  })
  
  # Heatmap
  nj_heatmap_title_val <- reactiveVal()
  nj_colnames_angle_val <- reactiveVal()
  nj_colnames_y_val <- reactiveVal()
  nj_heatmap_width_val <- reactiveVal()
  nj_heatmap_offset_reactive <- reactive({
    ifelse(!is.null(input$nj_heatmap_offset),
           input$nj_heatmap_offset,
           0)}) |> debounce(100)
  nj_heatmap_offset_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_heatmap_title),
           nj_heatmap_title_val(input$nj_heatmap_title),
           nj_heatmap_title_val("Heatmap"))
    
    ifelse(!is.null(input$nj_colnames_angle),
           nj_colnames_angle_val(input$nj_colnames_angle),
           ifelse(!is.null(nj_layout_val()),
                  ifelse(nj_layout_val() == "circular" | 
                           nj_layout_val() == "inward",
                         nj_colnames_angle_val(90),
                         nj_colnames_angle_val(-90)),
                  nj_colnames_angle_val(-90)))
    
    ifelse(!is.null(input$nj_colnames_y),
           nj_colnames_y_val(input$nj_colnames_y),
           ifelse(nj_layout_val() == "circular" | 
                    nj_layout_val() == "inward",
                  nj_colnames_y_val(0),
                  nj_colnames_y_val(-1)))
    
    ifelse(!is.null(input$nj_heatmap_width),
           nj_heatmap_width_val(input$nj_heatmap_width),
           nj_heatmap_width_val(heatmap_width()))
    
    nj_heatmap_offset_val(nj_heatmap_offset_reactive())
  })
  
  # Clade highlights
  nj_nodelabel_show_val <- reactiveVal()
  nj_parentnode_reactive <- reactive({
    if(!is.null(input$nj_parentnode)) {
      input$nj_parentnode} else {""}})|> debounce(100)
  nj_parentnode_val <- reactiveVal()  
  nj_clade_scale_val <- reactiveVal()
  nj_clade_type_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_nodelabel_show),
           nj_nodelabel_show_val(input$nj_nodelabel_show),
           nj_nodelabel_show_val(FALSE))
    
    nj_parentnode_val(nj_parentnode_reactive())
    
    ifelse(!is.null(input$nj_clade_scale),
           nj_clade_scale_val(input$nj_clade_scale),
           nj_clade_scale_val(clade_highlight_color()))
    
    ifelse(!is.null(input$nj_clade_type),
           nj_clade_type_val(input$nj_clade_type),
           nj_clade_type_val("roundrect"))  
  })
  
  
  ###### Elements Interface ----
  
  observeEvent(input$nj_elements_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_elements_menu")
    
    output$tree_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Elements Menu",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 8,
                    h4(p("Tip Points"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                ),
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_tippoint_show",
                        "",
                        value = isolate(nj_tippoint_show_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 3,
                  h5(p("Shape"), style = "color:white; position: relative; top: 19px; margin-bottom: -10px; right: -15px")
                ),
                column(
                  width = 6,
                  uiOutput("nj_tippoint_shape_ui")
                ),
                column(
                  width = 3,
                  dropMenu(
                    actionBttn(
                      "nj_tippoint_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        sliderInput(
                          "nj_tippoint_alpha",
                          label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                          value = isolate(nj_tippoint_alpha_val()),
                          min = 0.1,
                          step = 0.05,
                          max = 1,
                          width = "150px",
                          ticks = FALSE
                        ), 
                        br(),
                        sliderInput(
                          inputId = "nj_tippoint_size",
                          label = h5("Size", style = "color:white; margin-bottom: 0px"),
                          min = 1,
                          max = 20,
                          step = 0.5,
                          value = isolate(nj_tippoint_size_val()),
                          width = "150px",
                          ticks = FALSE
                        )
                      )
                    )
                  )
                )
              ),
              div(class = "nj-elements-hr", hr()),
              fluidRow(
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 8,
                    h4(p("Node Points"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                ),
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 4,
                    align = "center",
                    div(
                      class = "mat-switch-v",
                      materialSwitch(
                        "nj_nodepoint_show",
                        "",
                        value = isolate(nj_nodepoint_show_val())
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 3,
                  h5(p("Shape"), style = "color:white; position: relative; top: 19px; margin-bottom: -10px; right: -15px")
                ),
                column(
                  width = 6,
                  selectInput(
                    "nj_nodepoint_shape",
                    "",
                    choices = c(
                      Circle = "circle", 
                      Square = "square", 
                      Diamond = "diamond", 
                      Triangle = "triangle",
                      Cross = "cross", 
                      Asterisk = "asterisk"
                    ),
                    selected = isolate(nj_nodepoint_shape_val())
                  )
                ),
                column(
                  width = 3,
                  dropMenu(
                    actionBttn(
                      "nj_nodepoint_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        sliderInput(
                          "nj_nodepoint_alpha",
                          label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                          value = isolate(nj_nodepoint_alpha_val()),
                          min = 0.1,
                          step = 0.05,
                          max = 1,
                          width = "150px",
                          ticks = FALSE
                        ), 
                        br(),
                        sliderInput(
                          inputId = "nj_nodepoint_size",
                          label = h5("Size", style = "color:white; margin-bottom: 0px"),
                          min = 1,
                          max = 20,
                          value = isolate(nj_nodepoint_size_val()),
                          step = 0.5,
                          width = "150px",
                          ticks = FALSE
                        )
                      )
                    )
                  )
                )
              ),
              div(class = "nj-elements-hr", hr()),
              fluidRow(
                div(
                  class = "nj-elements-control-tiles",
                  column(
                    width = 4,
                    h4(p("Tiles"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                ),
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 5,
                    align = "left",
                    div(
                      class = "sel-tile-number",
                      selectInput(
                        "nj_tile_number",
                        "",
                        choices = 1:5,
                        width = "70px",
                        selected = isolate(nj_tile_number_val())
                      )
                    )
                  )
                ),
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 3,
                    dropMenu(
                      actionBttn(
                        "nj_tile_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right",
                      theme = "translucent",
                      fluidRow(
                        column(
                          width = 12,
                          align = "center",
                          conditionalPanel(
                            "input.nj_tile_number == 1",
                            sliderInput(
                              "nj_fruit_alpha",
                              label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                              min = 0.1,
                              max = 1,
                              value = isolate(nj_fruit_alpha_val()),
                              step = 0.05,
                              width = "150px",
                              ticks = FALSE
                            )
                          ),
                          conditionalPanel(
                            "input.nj_tile_number == 2",
                            sliderInput(
                              "nj_fruit_alpha_2",
                              label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                              min = 0.1,
                              max = 1,
                              value = isolate(nj_fruit_alpha_2_val()),
                              step = 0.05,
                              width = "150px",
                              ticks = FALSE
                            )
                          ),
                          conditionalPanel(
                            "input.nj_tile_number == 3",
                            sliderInput(
                              "nj_fruit_alpha_3",
                              label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                              min = 0.1,
                              max = 1,
                              value = isolate(nj_fruit_alpha_3_val()),
                              step = 0.05,
                              width = "150px",
                              ticks = FALSE
                            )
                          ),
                          conditionalPanel(
                            "input.nj_tile_number == 4",
                            sliderInput(
                              "nj_fruit_alpha_4",
                              label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                              min = 0.1,
                              max = 1,
                              value = isolate(nj_fruit_alpha_4_val()),
                              step = 0.05,
                              width = "150px",
                              ticks = FALSE
                            )
                          ),
                          conditionalPanel(
                            "input.nj_tile_number == 5",
                            sliderInput(
                              "nj_fruit_alpha_5",
                              label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
                              min = 0.1,
                              max = 1,
                              value = isolate(nj_fruit_alpha_5_val()),
                              step = 0.05,
                              width = "150px",
                              ticks = FALSE
                            )
                          )
                        )
                      )
                    )
                  )
                )
              ),
              conditionalPanel(
                "input.nj_tile_number == 1",
                fluidRow(
                  column(
                    width = 5,
                    h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_width")
                  )
                ),
                fluidRow(
                  column(
                    width = 5,
                    h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_offset_circ")
                  )
                )
              ),
              conditionalPanel(
                "input.nj_tile_number == 2",
                fluidRow(
                  column(
                    width = 5,
                    h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_width2")
                  )
                ),
                fluidRow(
                  column(
                    width = 5,
                    h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; ")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_offset_circ_2")
                  )
                )
              ),
              conditionalPanel(
                "input.nj_tile_number == 3",
                fluidRow(
                  column(
                    width = 5,
                    h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_width3")
                  )
                ),
                fluidRow(
                  column(
                    width = 5,
                    h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; ")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_offset_circ_3")
                  )
                )
              ),
              conditionalPanel(
                "input.nj_tile_num == 4",
                fluidRow(
                  column(
                    width = 5,
                    h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_width4")
                  )
                ),
                fluidRow(
                  column(
                    width = 5,
                    h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_offset_circ_4")
                  )
                )
              ),
              conditionalPanel(
                "input.nj_tile_number == 5",
                fluidRow(
                  column(
                    width = 5,
                    h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_width5")
                  )
                ),
                fluidRow(
                  column(
                    width = 5,
                    h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px;")
                  ),
                  column(
                    width = 7,
                    align = "center",
                    uiOutput("nj_fruit_offset_circ_5"),
                  )
                )
              ),
              div(class = "nj-elements-hr", hr()),
              fluidRow(
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 12,
                    h4(p("Heatmap"), style = "color:grey; position: relative; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 3,
                  h5("Title", style = "color:white; margin-left: 15px; margin-top: 15px;")
                ),
                column(
                  width = 6,
                  align = "left",
                  shinyjs::disabled(
                    textInput(
                      "nj_heatmap_title",
                      label = "",
                      value = isolate(nj_heatmap_title_val()),
                      placeholder = "Heatmap" 
                    )
                  )
                ),
                column(
                  width = 3,
                  dropMenu(
                    shinyjs::disabled(
                      actionBttn(
                        "nj_heatmap_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      )
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Angle')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              sliderInput(
                                "nj_colnames_angle",
                                label = "",
                                min = -90,
                                max = 90,
                                value = isolate(nj_colnames_angle_val()),
                                width = "150px",
                                ticks = FALSE
                              )
                            )
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Position')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              uiOutput("nj_colnames_y")
                            )
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Width')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              sliderInput(
                                "nj_heatmap_width",
                                label = "",
                                min = 0.05,
                                max = 1.5,
                                value = isolate(nj_heatmap_width_val()),
                                step = 0.05,
                                width = "150px",
                                ticks = FALSE
                              )
                            )
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Offset')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              uiOutput("nj_heatmap_offset")
                            )
                          )
                        )
                      )
                    )
                  )
                )
              ),
              div(class = "nj-elements-hr", hr()),
              fluidRow(
                div(
                  class = "nj-elements-control-col",
                  column(
                    width = 12,
                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  div(
                    class = "control-nodelabel-switch",
                    materialSwitch(
                      "nj_nodelabel_show",
                      h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(nj_nodelabel_show_val()),
                      right = TRUE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 3,
                  h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 14px")
                ),
                column(
                  width = 6,
                  uiOutput("nj_parentnode")
                ),
                column(
                  width = 3,
                  dropMenu(
                    actionBttn(
                      "nj_clade_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right-start",
                    theme = "translucent",
                    uiOutput("nj_clade_scale"),
                    fluidRow(
                      column(
                        width = 3,
                        h5(p("Form"), style = "color:white; position: relative; margin-top: 27px")
                      ),
                      column(
                        width = 9,
                        div(
                          class = "sel-clade",
                          selectInput(
                            "nj_clade_type",
                            "",
                            choices = c("Rect" = "rect",
                                        "Round" = "roundrect"),
                            selected = isolate(nj_clade_type_val()),
                            width = "150px"
                          ) 
                        )
                      )
                    )
                  )
                )
              )
            )
          )
        )
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ###### Elements Inputs ----
  
  # Tip points
  output$nj_tippoint_shape_ui <- renderUI({
    output <- render_plot_control(
      input_id = "nj_tippoint_shape",
      input_type = "selectInput",
      choices = c(Circle = "circle", Square = "square", Diamond = "diamond",
                  Triangle = "triangle", Cross = "cross",
                  Asterisk = "asterisk"),
      reactive_value = nj_tippoint_shape_val(),
      default_value = "circle",
      reset = isolate(Vis$nj_tippoint_shape_reset),
      show_condition = isFALSE(nj_tipshape_mapping_show_val()))

    isolate(Vis$nj_tippoint_shape_reset <- FALSE)
    
    output
  })
  
  # Heatmap settings
  output$nj_heatmap_offset <- renderUI({
    
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 1.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_heatmap_offset",
      input_type = "sliderInput",
      width = "150px",
      min = 0,
      max = max,
      step = 1,
      reactive_value = nj_heatmap_offset_val(),
      default_value = 0,
      reset = isolate(Vis$nj_heatmap_offset_val_reset))
    
    isolate(Vis$nj_heatmap_offset_val_reset <- FALSE)
    
    output
  })
  
  # Clade highlighting
  output$nj_parentnode <- renderUI({
    ifelse(!is.null(Vis$nj_parentnodes),
           choices <- sort(unique(as.numeric(Vis$nj_parentnodes))),
           choices <- "")
    
    output <- render_plot_control(
      input_id = "nj_parentnode",
      input_type = "pickerInput",
      multiple = TRUE,
      width = "99%",
      options = list(
        `live-search` = TRUE,
        size = 10,
        style = "background-color: white; border-radius: 5px;"
      ),
      choices = choices,
      reactive_value = nj_parentnode_val(),
      default_value = "",
      reset = isolate(Vis$nj_parentnode_val_reset))
    
    isolate(Vis$nj_parentnode_val_reset <- FALSE)
    
    output
  })
  
  output$nj_clade_scale <- renderUI({
    selected_nodes <- nj_parentnode_val()
    if (length(selected_nodes) == 1 && selected_nodes == "") selected_nodes <- NULL
    
    if (length(selected_nodes) < 2) {
      label <- "Color"

      ifelse(length(selected_nodes == 1),
             selected <- nj_clade_scale_val(),
             selected <- "#D0F221")

      nj_clade_scale <- colorPickr(
        inputId = "nj_clade_scale",
        selected = selected,
        label = "",
        update = "changestop",
        interaction = list(clear = FALSE,
                           save = FALSE),
        position = "right-start",
        width = "150px")
    } else {
      label <- "Scale"
      nj_clade_scale <- div(
        class = "sel-clade-scale",
        selectInput(
          "nj_clade_scale",
          "",
          choices = list(Qualitative = qualitative_scales,
                         Sequential = sequential_scales),
          selected = nj_clade_scale_val(),
          width = "150px")
      )
    }
    
    fluidRow(
      column(
        width = 3,
        h5(label, style = "color:white; position: relative; margin-top: 20px")
      ),
      column(
        width = 9,
        align = "center",
        nj_clade_scale
      )
    )
  })
  
  # Heatmap control
  output$nj_colnames_y <- renderUI({
    req(DB$data)
    
    disable <- FALSE
    if(nj_layout_val() == "inward" | 
       nj_layout_val() == "circular") {
      min <- 0
      disable <- TRUE
    } else {
      ifelse((sum(DB$data$Include) * -0.1) > -2,
             min <- -2,
             min <- round(sum(DB$data$Include) * -0.1, 0))
    }
    
    output <- render_plot_control(
      input_id = "nj_colnames_y",
      input_type = "sliderInput",
      width = "150px",
      step = 1,
      min = min,
      max = sum(DB$data$Include),
      reactive_value = nj_colnames_y_val(),
      default_value = -1,
      reset = isolate(Vis$nj_colnames_y_val_reset),
      show_condition = !disable)
    
    isolate(Vis$nj_colnames_y_val_reset <- FALSE)
    
    output
  })
  
  # Tiles settings
  
  output$nj_fruit_width <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_fruit_width_circ",
      input_type = "sliderInput",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_fruit_width_circ_val(),
      default_value = fruit_width(),
      reset = isolate(Vis$nj_fruit_width_circ_val_reset))
    
    isolate(Vis$nj_fruit_width_circ_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_width2 <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_fruit_width_circ_2",
      input_type = "selectInput",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_fruit_width_circ_2_val(),
      default_value = fruit_width(),
      reset = isolate(Vis$nj_fruit_width_circ_2_val_reset))
    
    isolate(Vis$nj_fruit_width_circ_2_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_width3 <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_fruit_width_circ_3",
      input_type = "selectInput",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_fruit_width_circ_3_val(),
      default_value = fruit_width(),
      reset = isolate(Vis$nj_fruit_width_circ_3_val_reset))
    
    isolate(Vis$nj_fruit_width_circ_3_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_width4 <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_fruit_width_circ_4",
      input_type = "selectInput",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_fruit_width_circ_4_val(),
      default_value = fruit_width(),
      reset = isolate(Vis$nj_fruit_width_circ_4_val_reset))
    
    isolate(Vis$nj_fruit_width_circ_4_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_width5 <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(ceiling(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_fruit_width_circ_5",
      input_type = "selectInput",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_fruit_width_circ_5_val(),
      default_value = fruit_width(),
      reset = isolate(Vis$nj_fruit_width_circ_5_val_reset))
    
    isolate(Vis$nj_fruit_width_circ_5_val_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_offset_circ <- renderUI({
    if(!is.null (nj_layout_val()) &&
       (nj_layout_val() == "circular" | nj_layout_val() == "inward")) {
      step <- 0.03
      min <- -0.6
      max <- 0.6
    } else {
      step <- 0.01
      min <- -0.2
      max <- 0.2
    }
    
    output <- render_plot_control(
      input_id = "nj_fruit_offset_circ",
      input_type = "sliderInput",
      width = "150px",
      step = step,
      min = min,
      max = max,
      reactive_value = nj_fruit_offset_circ_val(),
      default_value = 0.05,
      reset = isolate(Vis$nj_fruit_offset_circ_reset))
    
    isolate(Vis$nj_fruit_offset_circ_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_offset_circ_2 <- renderUI({
    if(!is.null (nj_layout_val()) &&
       (nj_layout_val() == "circular" | nj_layout_val() == "inward")) {
      step <- 0.03
      min <- -0.6
      max <- 0.6
    } else {
      step <- 0.01
      min <- -0.2
      max <- 0.2
    }
    
    output <- render_plot_control(
      input_id = "nj_fruit_offset_circ_2",
      input_type = "sliderInput",
      width = "150px",
      step = step,
      min = min,
      max = max,
      reactive_value = nj_fruit_offset_circ_2_val(),
      default_value = 0.05,
      reset = isolate(Vis$nj_fruit_offset_circ_2_reset))
    
    isolate(Vis$nj_fruit_offset_circ_2_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_offset_circ_3 <- renderUI({
    if(!is.null (nj_layout_val()) &&
       (nj_layout_val() == "circular" | nj_layout_val() == "inward")) {
      step <- 0.03
      min <- -0.6
      max <- 0.6
    } else {
      step <- 0.01
      min <- -0.2
      max <- 0.2
    }
    
    output <- render_plot_control(
      input_id = "nj_fruit_offset_circ_3",
      input_type = "sliderInput",
      width = "150px",
      step = step,
      min = min,
      max = max,
      reactive_value = nj_fruit_offset_circ_3_val(),
      default_value = 0.05,
      reset = isolate(Vis$nj_fruit_offset_circ_3_reset))
    
    isolate(Vis$nj_fruit_offset_circ_3_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_offset_circ_4 <- renderUI({
    if(!is.null (nj_layout_val()) &&
       (nj_layout_val() == "circular" | nj_layout_val() == "inward")) {
      step <- 0.03
      min <- -0.6
      max <- 0.6
    } else {
      step <- 0.01
      min <- -0.2
      max <- 0.2
    }
    
    output <- render_plot_control(
      input_id = "nj_fruit_offset_circ_4",
      input_type = "sliderInput",
      width = "150px",
      step = step,
      min = min,
      max = max,
      reactive_value = nj_fruit_offset_circ_4_val(),
      default_value = 0.05,
      reset = isolate(Vis$nj_fruit_offset_circ_4_reset))
    
    isolate(Vis$nj_fruit_offset_circ_4_reset <- FALSE)
    
    output
  })
  
  output$nj_fruit_offset_circ_5 <- renderUI({
    if(!is.null (nj_layout_val()) &&
       (nj_layout_val() == "circular" | nj_layout_val() == "inward")) {
      step <- 0.03
      min <- -0.6
      max <- 0.6
    } else {
      step <- 0.01
      min <- -0.2
      max <- 0.2
    }
    
    output <- render_plot_control(
      input_id = "nj_fruit_offset_circ_5",
      input_type = "sliderInput",
      width = "150px",
      step = step,
      min = min,
      max = max,
      reactive_value = nj_fruit_offset_circ_5_val(),
      default_value = 0.05,
      reset = isolate(Vis$nj_fruit_offset_circ_5_reset))
    
    isolate(Vis$nj_fruit_offset_circ_5_reset <- FALSE)
    
    output
  })
  
  
  ##### Other Menu ----
  
  ###### Other Control Values ----
  
  # Dimensions
  nj_ratio_val <- reactiveVal()
  nj_v_val <- reactiveVal()
  nj_h_val <- reactiveVal()
  nj_scale_val <- reactiveVal()
  nj_zoom_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_ratio),
           nj_ratio_val(input$nj_ratio),
           nj_ratio_val(c("16:10" = (16 / 10))))
    
    ifelse(!is.null(input$nj_v),
           nj_v_val(input$nj_v),
           nj_v_val(0))
    
    ifelse(!is.null(input$nj_h),
           nj_h_val(input$nj_h),
           ifelse(nj_layout_val() != "circular" &
                    nj_layout_val() != "inward",
                  nj_h_val(-0.05),
                  nj_h_val(0)))
    
    ifelse(!is.null(input$nj_scale),
           nj_scale_val(input$nj_scale),
           nj_scale_val(670))
    
    ifelse(!is.null(input$nj_zoom),
           nj_zoom_val(input$nj_zoom),
           nj_zoom_val(0.95))
  })
  
  # Layout
  nj_layout_val <- reactiveVal()
  nj_rootedge_show_val <- reactiveVal()
  nj_rootedge_length_reactive <- reactive({
    ifelse(!is.null(input$nj_rootedge_length),
           input$nj_rootedge_length,
           ifelse(!is.null(Vis$nj_max_x),
                  round(ceiling(Vis$nj_max_x) * 0.05),
                  2))}) |> debounce(100)
  nj_rootedge_length_val <- reactiveVal()
  nj_rootedge_line_val <- reactiveVal()
  nj_xlim_reactive <- reactive({
    ifelse(!is.null(input$nj_xlim),
           input$nj_xlim,
           -10)}) |> debounce(100)
  nj_xlim_val <- reactiveVal()
  nj_xlim_inw_reactive <- reactive({
    ifelse(!is.null(input$nj_xlim_inw),
           input$nj_xlim_inw,
           50)}) |> debounce(100)
  nj_xlim_inw_val <- reactiveVal()
  nj_treescale_show_val <- reactiveVal()
  nj_treescale_width_reactive <- reactive({
    ifelse(!is.null(input$nj_treescale_width),
           input$nj_treescale_width,
           ifelse(!is.null(Vis$nj_max_x),
                  round(ceiling(Vis$nj_max_x) * 0.1, 0),
                  2))}) |> debounce(100)
  nj_treescale_width_val <- reactiveVal()
  nj_treescale_x_reactive <- reactive({
    ifelse(!is.null(input$nj_treescale_x),
           input$nj_treescale_x,
           ifelse(!is.null(Vis$nj_max_x),
                  round(ceiling(Vis$nj_max_x) * 0.2, 0),
                  2))}) |> debounce(100)
  nj_treescale_x_val <- reactiveVal()
  nj_treescale_y_reactive <- reactive({
    ifelse(!is.null(input$nj_treescale_y),
           input$nj_treescale_y,
           0)}) |> debounce(100)
  nj_ladder_val <- reactiveVal()
  nj_treescale_y_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_layout),
                  nj_layout_val(input$nj_layout),
                  nj_layout_val("rectangular"))
    
    ifelse(!is.null(input$nj_rootedge_show),
           nj_rootedge_show_val(input$nj_rootedge_show),
           nj_rootedge_show_val(FALSE))
    
    nj_rootedge_length_val(nj_rootedge_length_reactive())
    
    ifelse(!is.null(input$nj_rootedge_line),
           nj_rootedge_line_val(input$nj_rootedge_line),
           nj_rootedge_line_val("solid"))
    
    nj_xlim_val(nj_xlim_reactive())
    
    nj_xlim_inw_val(nj_xlim_inw_reactive())
    
    ifelse(!is.null(input$nj_treescale_show),
           nj_treescale_show_val(input$nj_treescale_show),
           nj_treescale_show_val(FALSE))
    
    nj_treescale_width_val(nj_treescale_width_reactive())
    
    nj_treescale_x_val(nj_treescale_x_reactive())
    
    nj_treescale_y_val(nj_treescale_y_reactive())
    
    ifelse(!is.null(input$nj_ladder),
           nj_ladder_val(input$nj_ladder),
           nj_ladder_val(TRUE))})
  
  # Legend
  nj_legend_orientation_val <- reactiveVal()
  nj_legend_size_val <- reactiveVal()
  nj_legend_x_val <- reactiveVal()
  nj_legend_y_val <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$nj_legend_orientation),
           nj_legend_orientation_val(input$nj_legend_orientation),
           nj_legend_orientation_val("vertical"))
    
    ifelse(!is.null(input$nj_legend_size),
           nj_legend_size_val(input$nj_legend_size),
           nj_legend_size_val(10))
    
    ifelse(!is.null(input$nj_legend_x),
           nj_legend_x_val(input$nj_legend_x),
           nj_legend_x_val(0.9))
    
    ifelse(!is.null(input$nj_legend_y),
           nj_legend_y_val(input$nj_legend_y),
           nj_legend_y_val(0.2))
  })
  
  
  ###### Other Interface ----
  
  observeEvent(input$nj_misc_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_misc_menu")
    
    output$tree_controls <- renderUI({
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Miscellaneous",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    h4(p("Dimensions"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  h5(p("Ratio"), style = "color:white; position: relative; top: 19px; margin-bottom: -10px; right: -15px")
                ),
                column(
                  width = 4,
                  align = "center",
                  div(
                    class = "nj-control-ratio",
                    selectInput(
                      "nj_ratio",
                      "",
                      choices = c("16:10" = (16 / 10), "16:9" = (16 / 9), "4:3" = (4 / 3)),
                      selected = isolate(nj_ratio_val())
                    )
                  )
                ),
                column(
                  width = 3,
                  dropMenu(
                    actionBttn(
                      "nj_dim_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                          'Vertical')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              sliderInput(
                                "nj_v",
                                label = "",
                                min = -0.5,
                                max = 0.5,
                                step = 0.01,
                                value = isolate(nj_v_val()),
                                width = "150px",
                                ticks = FALSE
                              )
                            )
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                          'Horizontal')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            div(
                              class = "nj-label-slider",
                              sliderInput(
                                "nj_h",
                                label = "",
                                min = -0.5,
                                max = 0.5,
                                step = 0.01,
                                value = isolate(nj_h_val()),
                                width = "150px",
                                ticks = FALSE
                              )
                            )
                          )
                        )
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  h5("Scale", style = "color:white; margin-left: 15px; margin-top: 30px;")
                ),
                column(
                  width = 8,
                  align = "center",
                  sliderInput(
                    "nj_scale",
                    "",
                    min = 450,
                    max = 670,
                    step = 5,
                    value = isolate(nj_scale_val()),
                    width = "80%",
                    ticks = FALSE
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  h5("Zoom", style = "color:white; margin-left: 15px; margin-top: 32px;")
                ),
                column(
                  width = 8,
                  align = "center",
                  sliderInput(
                    "nj_zoom",
                    "",
                    min = 0.5,
                    max = 1.5,
                    step = 0.05,
                    value = isolate(nj_zoom_val()),
                    width = "80%",
                    ticks = FALSE
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 5,
                    h4(p("Layout"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                ),
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 7,
                    div(
                      class = "nj-layout-select",
                      selectInput(
                        inputId = "nj_layout",
                        label = "",
                        choices = list(
                          Linear = list(
                            "Rectangular" = "rectangular",
                            "Roundrect" = "roundrect",
                            "Slanted" = "slanted",
                            "Ellipse" = "ellipse"
                          ),
                          Circular = list("Circular" = "circular",
                                          "Inward" = "inward")
                        ),
                        selected = isolate(nj_layout_val()),
                        width = "90%"
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  div(
                    class = "mat-switch-layout3",
                    materialSwitch(
                      "nj_ladder",
                      h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(nj_ladder_val()),
                      right = TRUE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  div(
                    class = "mat-switch-layout",
                    materialSwitch(
                      "nj_rootedge_show",
                      h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(nj_rootedge_show_val()),
                      right = TRUE
                    )
                  )
                ),
                column(
                  width = 4,
                  align = "right",
                  dropMenu(
                    actionBttn(
                      "nj_rootedge_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Length')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            uiOutput("nj_rootedge_length")
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 3,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                                          'Line')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "center",
                            div(
                              class = "nj-rootedge-line",
                              selectInput(
                                "nj_rootedge_line",
                                label = "",
                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
                                selected = isolate(nj_rootedge_line_val()),
                                width = "100px"
                              )
                            )
                          )
                        )
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  align = "left",
                  div(
                    class = "mat-switch-layout2",
                    materialSwitch(
                      "nj_treescale_show",
                      h5(p("Tree Scale"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(nj_treescale_show_val()),
                      right = TRUE
                    )
                  )
                ),
                column(
                  width = 4,
                  align = "right",
                  dropMenu(
                    actionBttn(
                      "nj_treescale_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "right",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                          'Length')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            uiOutput("nj_treescale_width")
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                          'Horizontal')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            uiOutput("nj_treescale_x")
                          )
                        ),
                        br(),
                        fluidRow(
                          column(
                            width = 2,
                            align = "left",
                            HTML(
                              paste(
                                tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                          'Vertical')
                              )
                            )
                          ),
                          column(
                            width = 9,
                            align = "right",
                            uiOutput("nj_treescale_y")
                          )
                        )
                      )
                    )
                  )
                )
              ),
              fluidRow(
                fluidRow(
                  column(
                    width = 6,
                    h5("Circular Space", style = "color:white; margin-left: 29px; margin-top: 30px;")
                  ),
                  column(
                    width = 5,
                    align = "center",
                    uiOutput("nj_xlim_ui")
                  )
                )
              ),
              hr(),
              fluidRow(
                column(
                  width = 12,
                  align = "left",
                  fluidRow(
                    div(
                      class = "nj-label-control-col",
                      column(
                        width = 8,
                        h4(p("Legend"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                      )
                    )
                  ),
                  fluidRow(
                    column(
                      width = 7,
                      align = "left",
                      prettyRadioButtons(
                        "nj_legend_orientation",
                        "",
                        choices = c(Horizontal = "horizontal",
                                    Vertical = "vertical"),
                        selected = isolate(nj_legend_orientation_val()),
                        inline = FALSE
                      )
                    ),
                    column(
                      width = 5,
                      align = "right",
                      dropMenu(
                        actionBttn(
                          "nj_legend_menu",
                          label = "",
                          color = "default",
                          size = "sm",
                          style = "material-flat",
                          icon = icon("sliders")
                        ),
                        placement = "right",
                        theme = "translucent",
                        fluidRow(
                          column(
                            width = 12,
                            align = "center",
                            fluidRow(
                              column(
                                width = 2,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                              'Size')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  sliderInput(
                                    "nj_legend_size",
                                    label = "",
                                    min = 5,
                                    max = 25,
                                    step = 1,
                                    value = isolate(nj_legend_size_val()),
                                    width = "150px",
                                    ticks = FALSE
                                  )
                                )
                              )
                            ),
                            br(),
                            fluidRow(
                              column(
                                width = 2,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                              'Horizontal')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  sliderInput(
                                    "nj_legend_x",
                                    label = "",
                                    value = isolate(nj_legend_x_val()),
                                    min = -0.9,
                                    max = 1.9,
                                    step = 0.2,
                                    width = "150px",
                                    ticks = FALSE
                                  )
                                )
                              )
                            ),
                            br(),
                            fluidRow(
                              column(
                                width = 2,
                                align = "left",
                                HTML(
                                  paste(
                                    tags$span(style='color: white; font-size: 14px; position: relative; right: 10px; top: 7px;',
                                              'Vertical')
                                  )
                                )
                              ),
                              column(
                                width = 9,
                                align = "right",
                                div(
                                  class = "nj-label-slider",
                                  sliderInput(
                                    "nj_legend_y",
                                    label = "",
                                    value = isolate(nj_legend_y_val()),
                                    min = -1.5,
                                    max = 1.5,
                                    step = 0.1,
                                    width = "150px",
                                    ticks = FALSE
                                  )
                                )
                              )
                            )
                          )
                        )
                      )
                    ) 
                  )
                )
              )
            )
          )
        )
      )
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ###### Other Inputs ----
  
  # Layout settings
  output$nj_xlim_ui <- renderUI({
    
    if(nj_layout_val() == "inward") {
      input_id <- "nj_xlim_inw"
      min <- 30
      max <- 120
      value <- nj_xlim_inw_val()
      default <- 50
      reset <- Vis$nj_xlim_inw_val_reset
      # nj_xlim <- div(
      #   class = "nj-xlim",
      #   sliderInput(
      #     "nj_xlim_inw",
      #     label = "",
      #     min = 30,
      #     max = 120,
      #     value = nj_xlim_inw_val(),
      #     width = "150px",
      #     ticks = FALSE))
    } else {
      input_id <- "nj_xlim"
      min <- -50
      max <- 0
      value <- nj_xlim_val()
      default <- -10
      reset <- Vis$nj_xlim_val_reset
      # nj_xlim <- div(
      #   class = "nj-xlim", 
      #   sliderInput(
      #     "nj_xlim",
      #     label = "",
      #     min = -50,
      #     max = 0,
      #     value = nj_xlim_val(),
      #     width = "150px",
      #     ticks = FALSE))
    }
    
    # if(nj_layout_val() == "inward" |
    #    nj_layout_val() == "circular") {
    #   nj_xlim
    # } else {
    #   shinyjs::disabled(nj_xlim)
    # }
    
    output <- render_plot_control(
      input_id = input_id,
      input_type = "sliderInput",
      div_class = "nj-xlim",
      width = "150px",
      min = min,
      max = max,
      reactive_value = value,
      default_value = default,
      reset = reset,
      show_condition = nj_layout_val() == "inward" |
        nj_layout_val() == "circular")
    
    isolate(Vis$nj_xlim_inw_val_reset <- Vis$nj_xlim_val_reset <- FALSE)
    
    output
  })
  
  # Treescale 
  output$nj_treescale_width <- renderUI({
    ifelse(!is.null(Vis$nj_max_x),
           max <- round(floor(Vis$nj_max_x) * 0.5, 0),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_treescale_width",
      input_type = "sliderInput",
      div_class = "nj-label-slider",
      width = "150px",
      min = 1,
      max = max,
      reactive_value = nj_treescale_width_val(),
      default_value = ifelse(!is.null(Vis$nj_max_x),
                             round(ceiling(Vis$nj_max_x) * 0.1, 0),
                             2),
      reset = isolate(Vis$nj_treescale_width_val_reset))
    
    isolate(Vis$nj_treescale_width_val_reset <- FALSE)
    
    output
  })
  
  output$nj_treescale_x <- renderUI({
    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
      ifelse(ceiling(Vis$nj_min_x) < 1,
             min <- 1,
             min <- ceiling(Vis$nj_min_x))
      
      max <- round(floor(Vis$nj_max_x))
    } else {
      min <- 1
      max <- 10
    }
    
    output <- render_plot_control(
      input_id = "nj_treescale_x",
      input_type = "sliderInput",
      div_class = "nj-label-slider",
      width = "150px",
      min = min,
      max = max,
      reactive_value = nj_treescale_x_val(),
      default_value = ifelse(!is.null(Vis$nj_max_x),
                             round(ceiling(Vis$nj_max_x) * 0.2, 0),
                             2),
      reset = isolate(Vis$nj_treescale_x_val_reset))
    
    isolate(Vis$nj_treescale_x_val_reset <- FALSE)
    
    output
  })
  
  output$nj_treescale_y <- renderUI({
    
    ifelse(!is.null(sum(DB$data$Include)),
           max <- sum(DB$data$Include),
           max <- 10)
    
    output <- render_plot_control(
      input_id = "nj_treescale_y",
      input_type = "sliderInput",
      div_class = "nj-label-slider",
      width = "150px",
      min = 0,
      max = max,
      reactive_value = nj_treescale_y_val(),
      default_value = 0,
      reset = isolate(Vis$nj_treescale_y_val_reset))
    
    isolate(Vis$nj_treescale_y_val_reset <- FALSE)
    
    output
  })
  
  # Rootedge 
  output$nj_rootedge_length <- renderUI({
    if(!is.null(Vis$nj_max_x)) {
      if(round(ceiling(Vis$nj_max_x) * 0.02, 0) < 1) {
        min <- 1
      } else {
        min <- round(ceiling(Vis$nj_max_x) * 0.02, 0)
      }
      max <- round(ceiling(Vis$nj_max_x) * 0.2, 0)
    } else {
      min <- 1
      max <- 10
    }
    
    output <- render_plot_control(
      input_id = "nj_rootedge_length",
      input_type = "sliderInput",
      div_class = "nj-label-slider",
      width = "150px",
      min = min,
      max = max,
      reactive_value = nj_rootedge_length_val(),
      default_value = ifelse(!is.null(Vis$nj_max_x),
                             round(ceiling(Vis$nj_max_x) * 0.05),
                             2),
      reset = isolate(Vis$nj_rootedge_length_val_reset))
    
    isolate(Vis$nj_rootedge_length_val_reset <- FALSE)
    
    output
  })
  
  ##### Export Menu ----
  
  observeEvent(input$nj_download_menu, {
    
    session$sendCustomMessage('nj_reset_style', "")
    session$sendCustomMessage('nj_highlight', "nj_download_menu")
    
    output$tree_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Export",
          fluidRow(
            column(
              width = 12,
              align = "center",
              br(),
              fluidRow(
                br(),
                column(
                  width = 6,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; left: 15px;',
                                'Save plot as')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  div(
                    class = "filetype-mst",
                    selectInput(
                      inputId = "filetype_nj",
                      label = "",
                      choices = c("png", "jpeg", "bmp", "svg")
                    )
                  )
                )
              ),
              fluidRow(
                column(6),
                column(
                  width = 6,
                  downloadBttn(
                    "download_nj",
                    style = "simple",
                    label = "",
                    size = "sm",
                    icon =  icon("download"),
                    color = "primary"
                  )
                )
              ),
              hr(), 
              fluidRow(
                column(
                  width = 6,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; left: 15px; top: 17px',
                                'Print Report')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  actionButton(
                    "create_rep",
                    "",
                    icon = icon("file-waveform")
                  )
                )
              ),
              br(), br()
            ) 
          )
        )
      )
    ) 
  })
  
  
  ##### Tree Control Events ----
  
  # Reset all control inputs
  observeEvent(input$nj_reset, {
    showModal(
      div(
        class = "load-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'Resetting all plot control inputs will lead to loss of all current settings. Continue?',
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Reset Plot Settings",
          footer = tagList(
            modalButton("Cancel"),
            actionButton("nj_reset_confirm", "Reset", class = "btn btn-default")
          )
        )
      )
    )
  })
  
  # Reset control values
  observeEvent(input$nj_reset_confirm, {
      
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    removeModal()
    
    # Tip label
    Vis$nj_tiplab_val_reset <- TRUE
    nj_tiplab_val("Assembly Name")
    nj_tiplab_show_val(TRUE)
    Vis$nj_align_reset <- TRUE
    nj_align_val(FALSE)
    ifelse(!is.null(Vis$labelsize_nj),
           nj_tiplab_size_val(Vis$labelsize_nj),
           nj_tiplab_size_val(4))
    nj_tiplab_fontface_val("plain")
    nj_tiplab_alpha_val(1)
    nj_tiplab_position_val(0)
    Vis$nj_tiplab_angle_reset <- TRUE
    nj_tiplab_angle_val(0)
    
    # Label panels
    nj_geom_val(FALSE)
    nj_tiplab_labelradius_val(0.2)
    ifelse(!is.null(Vis$tiplab_padding_nj),
           nj_tiplab_padding_val(Vis$tiplab_padding_nj),
           nj_tiplab_padding_val(0.2))
    
    # Branch labels
    nj_show_branch_label_val(FALSE)
    ifelse(!is.null(Vis$branch_size_nj),
           nj_branch_size_val(Vis$branch_size_nj),
           nj_branch_size_val(4))
    Vis$nj_branch_label_val_reset <- TRUE
    nj_branch_label_val("Host")
    nj_branchlab_alpha_val(0.65)
    nj_branch_x_val(0)
    nj_branchlab_fontface_val("plain")
    nj_branch_labelradius_val(0.5)
    
    # Titles
    nj_title_val(NULL)
    nj_title_size_val(30)
    nj_subtitle_val(NULL)
    nj_subtitle_size_val(30)
    
    # Custom label
    Vis$nj_label_pos_x <- list()
    Vis$nj_label_pos_y <- list()
    Vis$nj_label_size <- list()
    Vis$custom_label_nj <- data.frame()
    
    # Tip label mapping
    nj_mapping_show_val(FALSE)
    Vis$nj_color_mapping_val_reset <- TRUE
    nj_color_mapping_val("Country")
    Vis$nj_tiplab_scale_reset <- TRUE
    nj_tiplab_scale_val(nj_tiplab_scale_val_default())
    Vis$nj_color_mapping_div_mid_reset <- TRUE
    nj_color_mapping_div_mid_val("Mean")
    
    # Tip points mapping
    nj_tipcolor_mapping_show_val(FALSE)
    Vis$nj_tipcolor_mapping_val_reset <- TRUE
    nj_tipcolor_mapping_val("Country")
    Vis$nj_tippoint_scale_val_reset <- TRUE
    nj_tippoint_scale_val(nj_tippoint_scale_val_default())
    Vis$nj_tipcolor_mapping_div_mid_reset <- TRUE
    nj_tipcolor_mapping_div_mid_val("Mean")
    
    # Tip shape mapping
    nj_tipshape_mapping_show_val(FALSE)
    Vis$nj_tipshape_mapping_val_reset <- TRUE
    nj_tipshape_mapping_val("Host")
    
    # Tiles mapping
    nj_tiles_show_1_val(FALSE)
    nj_tiles_show_2_val(FALSE)
    nj_tiles_show_3_val(FALSE)
    nj_tiles_show_4_val(FALSE)
    nj_tiles_show_5_val(FALSE)
    Vis$nj_fruit_variable_val_reset <- TRUE
    nj_fruit_variable_val("Isolation Date")
    Vis$nj_fruit_variable_2_val_reset <- TRUE
    nj_fruit_variable_2_val("Isolation Date")
    Vis$nj_fruit_variable_3_val_reset <- TRUE
    nj_fruit_variable_3_val("Isolation Date")
    Vis$nj_fruit_variable_4_val_reset <- TRUE
    nj_fruit_variable_4_val("Isolation Date")
    Vis$nj_fruit_variable_5_val_reset <- TRUE
    nj_fruit_variable_5_val("Isolation Date")
    Vis$nj_tiles_scale_1_reset <- TRUE
    nj_tiles_scale_1_val(nj_tiles_scale_1_val_default())
    Vis$nj_tiles_scale_2_reset <- TRUE
    nj_tiles_scale_2_val(nj_tiles_scale_2_val_default())
    Vis$nj_tiles_scale_3_reset <- TRUE
    nj_tiles_scale_3_val(nj_tiles_scale_3_val_default())
    Vis$nj_tiles_scale_4_reset <- TRUE
    nj_tiles_scale_4_val(nj_tiles_scale_4_val_default())
    Vis$nj_tiles_scale_5_reset <- TRUE
    nj_tiles_scale_5_val(nj_tiles_scale_5_val_default())
    Vis$nj_tiles_mapping_div_mid_1_reset <- TRUE
    nj_tiles_mapping_div_mid_1_val("Mean")
    Vis$nj_tiles_mapping_div_mid_2_reset <- TRUE
    nj_tiles_mapping_div_mid_2_val("Mean")
    Vis$nj_tiles_mapping_div_mid_3_reset <- TRUE
    nj_tiles_mapping_div_mid_3_val("Mean")
    Vis$nj_tiles_mapping_div_mid_4_reset <- TRUE
    nj_tiles_mapping_div_mid_4_val("Mean")
    Vis$nj_tiles_mapping_div_mid_5_reset <- TRUE
    nj_tiles_mapping_div_mid_5_val("Mean")
    
    nj_heatmap_show_val(FALSE)
    Vis$nj_heatmap_select_val_reset <- TRUE
    nj_heatmap_select_val(NULL)
    Vis$nj_heatmap_scale_reset <- TRUE
    nj_heatmap_scale_val(nj_heatmap_scale_val_default())
    Vis$nj_heatmap_div_mid_val_reset <- TRUE
    nj_heatmap_div_mid_val("Mean")
    
    # Color values
    nj_color_val("#000000")
    nj_bg_val("#ffffff")
    nj_title_color_val("#000000")
    nj_tiplab_color_val("#000000")
    nj_tiplab_fill_val("#84D9A0")
    nj_branch_label_color_val("#FFB7B7")
    nj_tippoint_color_val("#3A4657")
    nj_nodepoint_color_val("#3A4657")
    
    # Tip points
    nj_tippoint_show_val(FALSE)
    Vis$nj_tippoint_shape_reset <- TRUE
    nj_tippoint_shape_val("circle")
    nj_tippoint_alpha_val(0.5)
    ifelse(!is.null(Vis$tippointsize_nj),
           nj_tippoint_size_val(Vis$tippointsize_nj),
           nj_tippoint_size_val(4))
    
    # Node points
    nj_nodepoint_show_val(FALSE)
    nj_nodepoint_shape_val("circle")
    nj_nodepoint_alpha_val(1)
    ifelse(!is.null(Vis$nodepointsize_nj),
           nj_nodepoint_size_val(Vis$nodepointsize_nj),
           nj_nodepoint_size_val(2.5))
    
    # Tiles
    nj_tile_number_val(1)
    nj_fruit_alpha_val(1)
    nj_fruit_alpha_2_val(1)
    nj_fruit_alpha_3_val(1)
    nj_fruit_alpha_4_val(1)
    nj_fruit_alpha_5_val(1)
    Vis$nj_fruit_width_circ_val_reset <- TRUE
    nj_fruit_width_circ_val(fruit_width())
    Vis$nj_fruit_width_circ_2_val_reset <- TRUE
    nj_fruit_width_circ_2_val(fruit_width())
    Vis$nj_fruit_width_circ_3_val_reset <- TRUE
    nj_fruit_width_circ_3_val(fruit_width())
    Vis$nj_fruit_width_circ_4_val_reset <- TRUE
    nj_fruit_width_circ_4_val(fruit_width())
    Vis$nj_fruit_width_circ_5_val_reset <- TRUE
    nj_fruit_width_circ_5_val(fruit_width())
    Vis$nj_fruit_offset_circ_reset <- TRUE
    nj_fruit_offset_circ_val(0.05)
    Vis$nj_fruit_offset_circ_2_reset <- TRUE
    nj_fruit_offset_circ_2_val(0.05)
    Vis$nj_fruit_offset_circ_3_reset <- TRUE
    nj_fruit_offset_circ_3_val(0.05)
    Vis$nj_fruit_offset_circ_4_reset <- TRUE
    nj_fruit_offset_circ_4_val(0.05)
    Vis$nj_fruit_offset_circ_5_reset <- TRUE
    nj_fruit_offset_circ_5_val(0.05)
    
    # Heatmap
    nj_heatmap_title_val("Heatmap")
    nj_colnames_angle_val(-90)
    Vis$nj_colnames_y_val_reset <- TRUE
    nj_colnames_y_val(-1)
    nj_heatmap_width_val(heatmap_width())
    Vis$nj_heatmap_offset_val_reset <- TRUE
    nj_heatmap_offset_val(0)
    
    # Clade highlights
    nj_nodelabel_show_val(FALSE)
    Vis$nj_parentnode_val_reset <- TRUE
    nj_parentnode_val("")
    nj_clade_scale_val(clade_highlight_color())
    nj_clade_type_val("roundrect")
    
    # Dimensions
    nj_ratio_val(c("16:10" = (16 / 10)))
    nj_v_val(0)
    nj_h_val(-0.05)
    nj_scale_val(670)
    nj_zoom_val(0.95)
    nj_layout_val("rectangular")
    nj_rootedge_show_val(FALSE)
    Vis$nj_rootedge_length_val_reset <- TRUE
    ifelse(!is.null(Vis$nj_max_x),
           nj_rootedge_length_val(round(ceiling(Vis$nj_max_x) * 0.05)),
           nj_rootedge_length_val(2))
    nj_rootedge_line_val("solid")
    Vis$nj_xlim_val_reset <- TRUE
    nj_xlim_val(-10)
    Vis$nj_xlim_inw_val_reset <- TRUE
    nj_xlim_inw_val(50)
    nj_treescale_show_val(FALSE)
    Vis$nj_treescale_width_val_reset <- TRUE
    ifelse(!is.null(Vis$nj_max_x),
           nj_treescale_width_val(round(ceiling(Vis$nj_max_x) * 0.1, 0)),
           nj_treescale_width_val(2))
    Vis$nj_treescale_x_val_reset <- TRUE
    ifelse(!is.null(Vis$nj_max_x),
           nj_treescale_x_val(round(ceiling(Vis$nj_max_x) * 0.2, 0)),
           nj_treescale_x_val(2))
    Vis$nj_treescale_y_val_reset <- TRUE
    nj_treescale_y_val(0)
    nj_ladder_val(TRUE)
    
    # Legend
    nj_legend_orientation_val("vertical")
    nj_legend_size_val(10)
    nj_legend_x_val(0.9)
    nj_legend_y_val(0.2)
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  observeEvent(input$nj_heatmap_button, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          conditionalPanel(
            "input.nj_heatmap_map==='Variables'",
            fluidRow(
              br(), 
              column(
                width = 11,
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                      'Mapping metadata and custom variables.',
                      '</span>'
                    )
                  )
                )
              ),
              br()
            )
          ),
          conditionalPanel(
            "input.nj_heatmap_map==='AMR Profile'",
            fluidRow(
              br(), 
              column(
                width = 11,
                p(
                  HTML(
                    if(isTRUE(Screening$available)) {
                      paste0(
                        '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                        'Mapping <b>resistance, virulence and other genes </b> resulting from AMR Screening.',
                        '</span>'
                      )
                    } else {
                      paste0(
                        '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                        'Antimicrobial resistance screening not available for ', gsub("CM|PM", "", DB$scheme), ".",
                        '</span>'
                      )
                    }    
                  )
                )
              ),
              br()
            )
          ),
          br(),
          fluidRow(
            column(
              width = 11,
              fluidRow(
                column(
                  width = 6,
                  uiOutput("nj_heatmap_sel")
                ),
                column(
                  width = 6,
                  conditionalPanel(
                    "input.nj_heatmap_map==='AMR Profile'",
                    if(isTRUE(Screening$available)) {
                      div(
                        class = "switch-heatmap_cluster",
                        materialSwitch(
                          "nj_heatmap_cluster",
                          h5(p("Cluster Genes"), 
                             style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
                          value = TRUE,
                          right = TRUE)
                      )
                    }
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  br(),
                  uiOutput("nj_heatmap_var_warning")
                )
              )
            )
          ),
          title = fluidRow(
            column(
              width = 5,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; font-size: 20px; position: relative; top: 5px; margin-left: 10px;">',
                    'Heatmap',
                    '</span>'
                  )
                )
              )
            ),
            column(
              width = 5,
              radioGroupButtons(
                inputId = "nj_heatmap_map",
                label = "",
                choices = c("Variables",
                            "AMR Profile"),
                justified = TRUE
              )
            )
          ),
          footer = tagList(modalButton("Cancel"),
                           actionButton("nj_heatmap_confirm", "Apply", 
                                        class = "btn btn-default"))
        )
      )
    )
  })
  
  # Size scaling NJ
  observe({
    if(equals(nj_ratio_val(), "1.6")) {
      updateSliderInput(session, "nj_scale",
                        step = 5, value = 670, min = 450, max = 670)
    } else if(equals(nj_ratio_val(), "1.77777777777778")) {
      updateSliderInput(session, "nj_scale",
                        step = 9, value = 657, min = 450, max = 666)
    } else if(equals(nj_ratio_val(), "1.33333333333333")) {
      updateSliderInput(session, "nj_scale",
                        step = 3, value = 654, min = 450, max = 669)
    }
  })
  
  ### Custom Labels
  # Add custom label
  observeEvent(input$nj_add_new_label, {
    
    if(nchar(input$nj_new_label_name) > 0) {
      if(!(input$nj_new_label_name %in% Vis$custom_label_nj)) {
        Vis$custom_label_nj <- rbind(Vis$custom_label_nj, input$nj_new_label_name) 
        if(nrow(Vis$custom_label_nj) != 1) {
          updateSelectInput(session, "nj_custom_label_sel", selected = input$nj_new_label_name)
        }
      } else {
        show_toast(
          title = "Label already exists",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
      }
    } else {
      show_toast(
        title = "Min. 1 character",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    }
  })
  
  # Delete custom label
  observeEvent(input$nj_del_label, {
    req(Vis$custom_label_nj)
    if(nrow(Vis$custom_label_nj) > 1) {
      Vis$custom_label_nj <- Vis$custom_label_nj[-which(Vis$custom_label_nj[,1] == input$nj_custom_label_sel), , drop = FALSE]
    } else if (nrow(Vis$custom_label_nj) == 1) {
      Vis$nj_label_pos_x <- list()
      Vis$nj_label_pos_y <- list()
      Vis$nj_label_size <- list()
      Vis$custom_label_nj <- data.frame()
    }
  })
  
  # Apply custom label changes
  observeEvent(input$nj_cust_label_save, {
    req(Vis$nj_label_pos_y, Vis$nj_label_pos_x, 
        Vis$nj_label_size, input$nj_custom_label_sel)
    
    Vis$nj_label_pos_y[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_y")]]
    Vis$nj_label_pos_x[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_x")]]
    Vis$nj_label_size[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_size")]]
  })
  
  # Update value if new variables added
  observeEvent(input$nj_heatmap_select, {
    req(nj_layout_val())
    
    length_input <- length(input$nj_heatmap_select)
    if(nj_layout_val() != "circular" & 
       nj_layout_val() != "inward") {
      if(length_input < 3) {
        width <- 0.1
      } else {
        if (length_input >= 3 && length_input <= 50) {
          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
        } else {
          width <- 1.5
        }   
      }
    } else {
      if(length_input < 3) {
        width <- 0.3
      } else if (length_input >= 3 && length_input <= 27) {
        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
      } else {
        width <- 3
      }
    }
    updateSliderInput(session, "nj_heatmap_width", value = width)
  })
  
  # Changes when tree layout changes
  observeEvent(input$nj_layout, {
    
    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
          width <- 3
        } else {
          width <- 1
        }
      } else {
        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
        } else {
          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
        }
      }
      
      nj_fruit_width_circ_val(width)
      nj_fruit_width_circ_2_val(width)
      nj_fruit_width_circ_3_val(width)
      nj_fruit_width_circ_4_val(width)
      nj_fruit_width_circ_5_val(width)
    }
    
    # if(input$nj_layout == "circular" | input$nj_layout == "inward") {
    #   offset <- 0.05
    #   step <- 0.01
    #   min <- -0.2
    #   max <- 0.2
    # } else {
    #   offset <- 0.15
    #   step <- 0.03
    #   min <- -0.6
    #   max <- 0.6
    # }
    # 
    # updateSliderInput(session, "nj_fruit_offset_circ", min = min, step = step, max = max)
    # updateSliderInput(session, "nj_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
    # updateSliderInput(session, "nj_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
    # updateSliderInput(session, "nj_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
    # updateSliderInput(session, "nj_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
    
    #
    
    if(input$nj_layout != "inward" & input$nj_layout != "circular") {
      # nj_colnames_angle_val(-90)
      # updateSliderInput(session, "nj_colnames_angle", value = -90)
      # nj_colnames_y_val(-1)
      
      if(!is.null(Vis$tree_algo) && Vis$tree_algo == "NJ") nj_align_val(FALSE)
      
      nj_h_val(-0.05)
      updateSliderInput(session, "nj_h", value = -0.05)
      
      nj_zoom_val(0.95)
      updateSliderInput(session, "nj_zoom", value = 0.95)
    } else {
      # nj_colnames_angle_val(90)
      # updateSliderInput(session, "nj_colnames_angle", value = 90)
      # nj_colnames_y_val(0)
      
      nj_align_val(TRUE)
      
      nj_h_val(0)
      updateSliderInput(session, "nj_h", value = 0)
      
      nj_v_val(0.03)
      updateSliderInput(session, "nj_v", value = 0.03)
    }
    
    # Adapt heatmap control inputs
    
    # length_input <- length(nj_heatmap_select_val())
    # 
    # if(input$nj_layout != "circular" & input$nj_layout != "inward") {
    #   if(length_input < 3) {
    #     width <- 0.1
    #   } else {
    #     if (length_input >= 3 && length_input <= 50) {
    #       width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
    #     } else {
    #       width <- 1.5
    #     }   
    #   }
    # } else {
    #   if(length_input < 3) {
    #     width <- 0.3
    #   } else if (length_input >= 3 && length_input <= 27) {
    #     width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
    #   } else {
    #     width <- 3
    #   }
    # }
    # 
    # nj_heatmap_width_val(width)
  })
  
  # Tile number selector update each other
  observeEvent(input$nj_tile_num, {
    updateSelectInput(session, "nj_tile_number", selected = input$nj_tile_num)
  })
  
  observeEvent(input$nj_tile_number, {
    updateSelectInput(session, "nj_tile_num", selected = input$nj_tile_number)
  })
  
  
  #### MST controls ----
  
  session$sendCustomMessage('mst_reset_style', "")
  session$sendCustomMessage('mst_highlight', "mst_label_menu")
  
  output$mst_controls <- renderUI(
    box(
      solidHeader = TRUE,
      status = "primary",
      width = "100%",
      title = "Labels",
      fluidRow(
        column(
          width = 12,
          align = "left",
          h4(p("Isolate Label"), style = "color:white; position: relative; right: -15px; top: 15px;"),
          column(
            width = 12,
            align = "center",
            div(
              class = "mst-label-sel",
              uiOutput("mst_node_label")
            )
          )
        )
      ),
      br(),
      fluidRow(
        column(
          width = 12,
          align = "left",
          h4(p("Title"), style = "color:white; position: relative; right: -15px; top: 15px;"),
          column(
            width = 12,
            align = "center",
            textInput(
              "mst_title",
              label = "",
              width = "100%",
              placeholder = "Plot Title"
            )
          )
        )
      ),
      br(),
      fluidRow(
        column(
          width = 12,
          align = "left",
          h4(p("Subtitle"), style = "color:white; position: relative; right: -15px; top: 15px;"),
          column(
            width = 12,
            align = "center",
            textInput(
              "mst_subtitle",
              label = "",
              width = "100%",
              placeholder = "Plot Subtitle"
            )
          )
        )
      ),
      br(), br()
    )
  )
  
  ##### Label Menu ----
  
  mst_node_label_reactive <- reactiveVal()
  mst_title_reactive <- reactiveVal()
  mst_subtitle_reactive <- reactiveVal()

  observe({
    #req(mst_color_var_reactive())
    
    ifelse(isTRUE(mst_color_var_reactive()),
           mst_node_label_reactive("Assembly Name"),
           ifelse(!is.null(input$mst_node_label),
                  mst_node_label_reactive(input$mst_node_label),
                  mst_node_label_reactive("Assembly Name")))
    
    ifelse(!is.null(input$mst_title),
           mst_title_reactive(input$mst_title),
           mst_title_reactive(""))
    
    ifelse(!is.null(input$mst_subtitle),
           mst_subtitle_reactive(input$mst_subtitle),
           mst_subtitle_reactive(""))
  })
  
  observeEvent(input$mst_label_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_label_menu")
    
    output$mst_controls <- renderUI(
      box(
        solidHeader = TRUE,
        status = "primary",
        width = "100%",
        title = "Labels",
        fluidRow(
          column(
            width = 12,
            align = "left",
            h4(p("Isolate Label"), style = "color:white; position: relative; right: -15px; top: 15px;"),
            column(
              width = 12,
              align = "center",
              div(
                class = "mst-label-sel",
                uiOutput("mst_node_label")
              )
            )
          )
        ),
        br(),
        fluidRow(
          column(
            width = 12,
            align = "left",
            h4(p("Title"), style = "color:white; position: relative; right: -15px; top: 15px;"),
            column(
              width = 12,
              align = "center",
              textInput(
                "mst_title",
                value = isolate(mst_title_reactive()),
                label = "",
                width = "100%",
                placeholder = "Plot Title"
              )
            )
          )
        ),
        br(),
        fluidRow(
          column(
            width = 12,
            align = "left",
            h4(p("Subtitle"), style = "color:white; position: relative; right: -15px; top: 15px;"),
            column(
              width = 12,
              align = "center",
              textInput(
                "mst_subtitle",
                value = isolate(mst_subtitle_reactive()),
                label = "",
                width = "100%",
                placeholder = "Plot Subtitle"
              )
            )
          )
        ),
        br(), br()
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ##### Variable Mapping Menu ----
  
  mst_color_var_reactive <- reactiveVal()
  mst_col_var_reactive <- reactiveVal()
  mst_col_scale_reactive <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$mst_color_var),
           mst_color_var_reactive(input$mst_color_var),
           mst_color_var_reactive(FALSE))
    
    ifelse(!is.null(input$mst_col_var),
           mst_col_var_reactive(input$mst_col_var),
           mst_col_var_reactive("Isolation Date"))
    
    ifelse(!is.null(input$mst_col_scale),
           mst_col_scale_reactive(input$mst_col_scale),
           mst_col_scale_reactive("Viridis"))
  })
  
  observeEvent(input$mst_variable_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_variable_menu")
    
    output$mst_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Variable Mapping",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                column(
                  width = 8,
                  align = "left",
                  h4(p("Node Color"), style = "color:white; position: relative; right: -15px; "),
                  bslib::tooltip(
                    bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
                                     height = "14px", width = "14px", position = "relative", right = "-120px"),
                    "Text shown in the tooltip.",
                    show = FALSE,
                    id = "mst_node_col_info"
                  )
                ),
                column(
                  width = 4,
                  align = "center",
                  div(
                    class = "mat-switch-v",
                    materialSwitch(
                      "mst_color_var",
                      "",
                      value = isolate(mst_color_var_reactive())
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 7,
                  div(
                    class = "mst-color-mapping",
                    selectInput(
                      "mst_col_var",
                      "",
                      choices = if(any(DB$cust_var[DB$cust_var$Variable[which(DB$cust_var$Variable %in% c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)]))],]$Type != "categ")) {
                        selection <- c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])
                        cust_vars <- DB$cust_var$Variable[which(DB$cust_var$Variable %in% selection)]
                        selection[-which(selection == cust_vars[DB$cust_var[cust_vars,]$Type != "categ"])]
                      } else {c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])},,
                      selected = isolate(mst_col_var_reactive()),
                      width = "100%"
                    )
                  )
                ),
                column(
                  width = 5,
                  div(
                    class = "mst-color-scale",
                    selectInput(
                      "mst_col_scale",
                      "",
                      choices = c("Viridis", "Rainbow"),
                      selected = isolate(mst_col_scale_reactive()),
                      width = "100%"
                    ) 
                  )
                )
              ),
              br()
            )
          )
        )
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ##### Color Menu ----
  
  mst_text_color_reactive <- reactiveVal()
  mst_color_node_reactive <- reactiveVal()
  mst_color_edge_reactive <- reactiveVal()
  mst_edge_font_color_reactive <- reactiveVal()
  mst_background_color_reactive <- reactiveVal()
  mst_background_transparent_reactive <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$mst_text_color),
           mst_text_color_reactive(input$mst_text_color),
           mst_text_color_reactive("#000000"))
    
    ifelse(!is.null(input$mst_color_node),
           mst_color_node_reactive(input$mst_color_node),
           mst_color_node_reactive("#B2FACA"))
    
    ifelse(!is.null(input$mst_color_edge),
           mst_color_edge_reactive(input$mst_color_edge),
           mst_color_edge_reactive("#000000"))
    
    ifelse(!is.null(input$mst_edge_font_color),
           mst_edge_font_color_reactive(input$mst_edge_font_color),
           mst_edge_font_color_reactive("#000000"))
    
    ifelse(!is.null(input$mst_background_color),
           mst_background_color_reactive(input$mst_background_color),
           mst_background_color_reactive("#ffffff"))
    
    ifelse(!is.null(input$mst_background_transparent),
           mst_background_transparent_reactive(input$mst_background_transparent),
           mst_background_transparent_reactive(FALSE))
  })
  
  observeEvent(input$mst_color_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_color_menu")
    
    output$mst_controls <- renderUI(
      box(
        solidHeader = TRUE,
        status = "primary",
        width = "100%",
        title = "Color Menu",
        column(
          width = 12,
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Text')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              colorPickr(
                inputId = "mst_text_color",
                selected = isolate(mst_text_color_reactive()),
                label = "",
                update = "changestop",
                interaction = list(clear = FALSE,
                                   save = FALSE),
                position = "right-start",
                width = "100%"
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Nodes')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              uiOutput("mst_color_mapping")
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Edges')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              colorPickr(
                inputId = "mst_color_edge",
                width = "100%",
                selected = isolate(mst_color_edge_reactive()),
                label = "",
                update = "changestop",
                interaction = list(clear = FALSE,
                                   save = FALSE),
                position = "right-start"
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Edge Font')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              colorPickr(
                inputId = "mst_edge_font_color",
                width = "100%",
                selected = isolate(mst_edge_font_color_reactive()),
                label = "",
                update = "changestop",
                interaction = list(clear = FALSE,
                                   save = FALSE),
                position = "right-start"
              )
            )
          ),
          br(),
          fluidRow(
            column(
              width = 6,
              align = "left",
              HTML(
                paste(
                  tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                            'Background')
                )
              )
            ),
            column(
              width = 6,
              align = "center",
              colorPickr(
                inputId = "mst_background_color",
                width = "100%",
                selected = isolate(mst_background_color_reactive()),
                label = "",
                update = "changestop",
                interaction = list(clear = FALSE,
                                   save = FALSE),
                position = "right-start"
              )
            )
          ), 
          fluidRow(
            column(1),
            column(
              width = 11,
              div(
                class = "switch-mst-transparent",
                materialSwitch(
                  "mst_background_transparent",
                  h5(p("Transparent"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                  value = isolate(mst_background_transparent_reactive()),
                  right = TRUE
                )
              )
            )
          ),
          br()
        )
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ##### Sizing Menu ----
  
  mst_scale_nodes_reactive <- reactiveVal()
  mst_node_scale_reactive <- reactiveVal()
  mst_node_size_reactive <- reactiveVal()
  mst_scale_edges_reactive <- reactiveVal()
  mst_edge_length_scale_reactive <- reactiveVal()
  mst_edge_length_reactive <- reactiveVal()
  mst_edge_font_size_reactive <- reactiveVal()
  mst_title_size_reactive <- reactiveVal()
  mst_subtitle_size_reactive <- reactiveVal()
  mst_node_label_fontsize_reactive <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$mst_scale_nodes),
           mst_scale_nodes_reactive(input$mst_scale_nodes),
           mst_scale_nodes_reactive(TRUE))
    
    ifelse(!is.null(input$mst_node_scale),
           mst_node_scale_reactive(input$mst_node_scale),
           mst_node_scale_reactive(c(20, 40)))
    
    ifelse(!is.null(input$mst_node_size),
           mst_node_size_reactive(input$mst_node_size),
           mst_node_size_reactive(30))
    
    ifelse(!is.null(input$mst_scale_edges),
           mst_scale_edges_reactive(input$mst_scale_edges),
           mst_scale_edges_reactive(TRUE))
    
    ifelse(!is.null(input$mst_edge_length_scale),
           mst_edge_length_scale_reactive(input$mst_edge_length_scale),
           mst_edge_length_scale_reactive(15))
    
    ifelse(!is.null(input$mst_edge_length),
           mst_edge_length_reactive(input$mst_edge_length),
           mst_edge_length_reactive(35))
    
    ifelse(!is.null(input$mst_edge_font_size),
           mst_edge_font_size_reactive(input$mst_edge_font_size),
           mst_edge_font_size_reactive(18))
    
    ifelse(!is.null(input$mst_node_label_fontsize),
           mst_node_label_fontsize_reactive(input$mst_node_label_fontsize),
           mst_node_label_fontsize_reactive(14))
    
    ifelse(!is.null(input$mst_title_size),
           mst_title_size_reactive(input$mst_title_size),
           mst_title_size_reactive(35))
    
    ifelse(!is.null(input$mst_subtitle_size),
           mst_subtitle_size_reactive(input$mst_subtitle_size),
           mst_subtitle_size_reactive(20))
  })
  
  observeEvent(input$mst_size_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_size_menu")
    
    output$mst_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Size Settings",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    h4(p("Nodes"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  align = "left",
                  div(
                    class = "switch-mst-edges",
                    materialSwitch(
                      "mst_scale_nodes",
                      h5(p("Scale by Duplicates"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(mst_scale_nodes_reactive()),
                      right = TRUE
                    )
                  ) 
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  align = "left",
                  fluidRow(
                    column(
                      width = 4,
                      conditionalPanel(
                        "input.mst_scale_nodes==true",
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -17px; margin-left: 15px ', 'Range')
                          )
                        )
                      ),
                      conditionalPanel(
                        "input.mst_scale_nodes==false",
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -17px; margin-left: 15px ', 'Size')
                          )
                        )
                      )
                    ),
                    column(
                      width = 8,
                      align = "center",
                      conditionalPanel(
                        "input.mst_scale_nodes==true",
                        div(
                          class = "mst_scale_slider",
                          sliderInput(
                            "mst_node_scale",
                            label = "",
                            min = 1,
                            max = 80,
                            value = isolate(mst_node_scale_reactive()),
                            ticks = FALSE
                          )
                        )
                      ),
                      conditionalPanel(
                        "input.mst_scale_nodes==false",
                        div(
                          class = "mst_scale_slider",
                          sliderInput(
                            inputId = "mst_node_size",
                            label = "",
                            min = 1,
                            max = 100,
                            value = isolate(mst_node_size_reactive()),
                            ticks = FALSE
                          ) 
                        )
                      )
                    )
                  ),
                  br()
                )  
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 8,
                    h4(p("Edges"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  div(
                    class = "switch-mst-edges",
                    materialSwitch(
                      "mst_scale_edges",
                      h5(p("Scale Allelic Distance"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(mst_scale_edges_reactive()),
                      right = TRUE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  conditionalPanel(
                    "input.mst_scale_edges==true",
                    HTML(
                      paste(
                        tags$span(style='color: white; font-size: 14px; position: relative; bottom: -17px; margin-left: 15px ', 'Multiplier')
                      )
                    )
                  ),
                  conditionalPanel(
                    "input.mst_scale_edges==false",
                    HTML(
                      paste(
                        tags$span(style='color: white; font-size: 14px; position: relative; bottom: -17px; margin-left: 15px ', 'Length')
                      )
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  conditionalPanel(
                    "input.mst_scale_edges==true",
                    div(
                      class = "slider_edge",
                      sliderInput(
                        inputId = "mst_edge_length_scale",
                        label = NULL,
                        min = 1,
                        max = 40,
                        value = isolate(mst_edge_length_scale_reactive()),
                        ticks = FALSE
                      ) 
                    )
                  ),
                  conditionalPanel(
                    "input.mst_scale_edges==false",
                    div(
                      class = "slider_edge",
                      sliderTextInput(
                        inputId = "mst_edge_length",
                        label = NULL,
                        choices = append(seq(0.1, 1, 0.1), 2:100),
                        selected = isolate(mst_edge_length_reactive()),
                        hide_min_max = FALSE
                      ) 
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; top: 7px; margin-left: 15px;',
                                'Font')
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  div(
                    class = "mst-edge-slider",
                    sliderInput(
                      "mst_edge_font_size",
                      "",
                      value = isolate(mst_edge_font_size_reactive()),
                      step = 1,
                      min = 8,
                      max = 30,
                      ticks = FALSE
                    )
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; top: 15px; margin-left: 15px;',
                                'Label') 
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  div(
                    class = "mst-size-slider",
                    sliderInput(
                      "mst_node_label_fontsize",
                      "",
                      value = isolate(mst_node_label_fontsize_reactive()),
                      min = 8,
                      max = 30,
                      step = 1,
                      ticks = FALSE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; top: 15px; margin-left: 15px;',
                                'Title')
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  div(
                    class = "mst-size-slider",
                    sliderInput(
                      "mst_title_size",
                      "",
                      value = isolate(mst_title_size_reactive()),
                      min = 15,
                      max = 50,
                      step = 1,
                      ticks = FALSE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; top: 15px; margin-left: 15px;',
                                'Subtitle')
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  div(
                    class = "mst-size-slider2",
                    sliderInput(
                      "mst_subtitle_size",
                      "",
                      value = isolate(mst_subtitle_size_reactive()),
                      min = 15,
                      max = 40,
                      step = 1,
                      ticks = FALSE
                    )
                  )
                )
              )
            )
          )
        )
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ##### Other Menu ----
  
  mst_ratio_reactive <- reactiveVal()
  mst_scale_reactive <- reactiveVal()
  mst_shadow_reactive <- reactiveVal()
  mst_node_shape_reactive <- reactiveVal()
  mst_show_clusters_reactive <- reactiveVal()
  mst_cluster_col_scale_reactive <- reactiveVal()
  mst_cluster_type_reactive <- reactiveVal()
  mst_cluster_width_reactive <- reactiveVal()
  mst_cluster_threshold_reactive <- reactiveVal()
  mst_legend_ori_reactive <- reactiveVal()
  mst_font_size_reactive <- reactiveVal()
  mst_symbol_size_reactive <- reactiveVal()
  
  observe({
    ifelse(!is.null(input$mst_ratio),
           mst_ratio_reactive(input$mst_ratio),
           mst_ratio_reactive(16/10))
    
    ifelse(!is.null(input$mst_scale),
           mst_scale_reactive(input$mst_scale),
           mst_scale_reactive(600))
    
    ifelse(!is.null(input$mst_shadow),
           mst_shadow_reactive(input$mst_shadow),
           mst_shadow_reactive(TRUE))
    
    ifelse(isTRUE(mst_color_var_reactive()),
           mst_node_shape_reactive("custom"),
           ifelse(!is.null(input$mst_node_shape),
                  mst_node_shape_reactive(input$mst_node_shape),
                  mst_node_shape_reactive("dot")))
    
    ifelse(!is.null(input$mst_show_clusters),
           mst_show_clusters_reactive(input$mst_show_clusters),
           mst_show_clusters_reactive(FALSE))
    
    ifelse(!is.null(input$mst_cluster_col_scale),
           mst_cluster_col_scale_reactive(input$mst_cluster_col_scale),
           mst_cluster_col_scale_reactive("Viridis"))
    
    ifelse(!is.null(input$mst_cluster_type),
           mst_cluster_type_reactive(input$mst_cluster_type),
           mst_cluster_type_reactive("Area"))
    
    ifelse(!is.null(input$mst_cluster_width),
           mst_cluster_width_reactive(input$mst_cluster_width),
           mst_cluster_width_reactive(24))
    
    ifelse(!is.null(input$mst_cluster_threshold),
           mst_cluster_threshold_reactive(input$mst_cluster_threshold),
           ifelse(!is.null(DB$cluster_thresh),
                  mst_cluster_threshold_reactive(DB$cluster_thresh),
                  mst_cluster_threshold_reactive(10)))
    
    ifelse(!is.null(input$mst_legend_ori),
           mst_legend_ori_reactive(input$mst_legend_ori),
           mst_legend_ori_reactive("left"))
    
    ifelse(!is.null(input$mst_font_size),
           mst_font_size_reactive(input$mst_font_size),
           mst_font_size_reactive(18))
    
    ifelse(!is.null(input$mst_symbol_size),
           mst_symbol_size_reactive(input$mst_symbol_size),
           mst_symbol_size_reactive(20))
  })
  
  observeEvent(input$mst_misc_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_misc_menu")
    
    output$mst_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Miscellaneous",
          fluidRow(
            column(
              width = 12,
              align = "left",
              br(),
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 12,
                    align = "left",
                    h4(p("Dimensions"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 5,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; margin-left: 15px; position: relative; top: 27px',
                                'Ratio')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  div(
                    class = "mst-control-ratio",
                    selectInput(
                      "mst_ratio",
                      "",
                      choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3)),
                      selected = isolate(mst_ratio_reactive())
                    )
                  )
                )
              ),
              br(),
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; margin-left: 15px; font-size: 14px; position: relative;',
                                'Scale')
                    )
                  )
                ),
                column(
                  width = 8,
                  align = "center",
                  div(
                    class = "mst-scale-slider",
                    sliderInput(
                      "mst_scale",
                      "",
                      min = 450,
                      max = 670,
                      step = 5,
                      value = isolate(mst_scale_reactive()),
                      ticks = FALSE
                    )
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 12,
                    align = "left",
                    h4(p("Node Shapes"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 12,
                  div(
                    class = "switch-mst-edges",
                    materialSwitch(
                      "mst_shadow",
                      h5(p("Show Shadow"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(mst_shadow_reactive()),
                      right = TRUE
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 5,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; margin-left: 15px; font-size: 14px; position: relative; top: 22px', 'Shape')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  div(
                    class = "mst-shape",
                    uiOutput("mst_node_shape")
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 12,
                    align = "left",
                    h4(p("Clustering"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px;"),
                    bslib::tooltip(
                      bsicons::bs_icon("info-circle", 
                                       title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
                                       color = "white", height = "15px", width = "15px", 
                                       position = "relative", top = "-21px", right = "-115px"),
                      "Text shown in the tooltip.",
                      show = FALSE,
                      id = "mst_cluster_info"
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  div(
                    class = "mst-cluster-switch",
                    materialSwitch(
                      "mst_show_clusters",
                      h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                      value = isolate(mst_show_clusters_reactive()),
                      right = TRUE
                    )
                  )
                ),
                column(
                  width = 3,
                  align = "right",
                  dropMenu(
                    actionBttn(
                      "mst_cluster_col_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "top-start",
                    theme = "translucent",
                    width = 5,
                    fluidRow(
                      column(
                        width = 12,
                        align = "center",
                        selectInput(
                          "mst_cluster_col_scale",
                          label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
                          choices = c("Viridis", "Rainbow"),
                          selected = isolate(mst_cluster_col_scale_reactive()),
                          width = "150px"
                        ),
                        br(),
                        selectInput(
                          "mst_cluster_type",
                          label = h5("Cluster Type", style = "color:white; margin-bottom: 0px;"),
                          choices = c("Area", "Skeleton"),
                          selected = isolate(mst_cluster_type_reactive()),
                          width = "150px"
                        ),
                        br(),
                        conditionalPanel(
                          "input.mst_cluster_type=='Skeleton'",
                          sliderInput(
                            "mst_cluster_width",
                            label = h5("Skeleton Width", style = "color:white; margin-bottom: 0px;"),
                            value = isolate(mst_cluster_width_reactive()),
                            step = 1,
                            min = 1,
                            max = 50,
                            ticks = FALSE,
                            width = "150px"
                          )
                        )
                      )
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 4,
                  HTML(
                    paste(
                      tags$span(style='color: white; margin-left: 15px; text-align: left; font-size: 14px;', 'Threshold')
                    )
                  )
                ),
                column(
                  width = 5,
                  uiOutput("mst_cluster")
                ),
                column(
                  width = 2,
                  align = "right",
                  div(
                    id = "mst_cluster_reset_div",
                    actionButton(
                      "mst_cluster_reset",
                      label = "",
                      icon = icon("rotate")
                    ),
                    addTooltip(session, id = 'mst_cluster_reset', 
                               title = "Labels",
                               placement = "bottom", trigger = "hover", 
                               options = list(delay = list(show = 400, hide = 300)))
                  )
                )
              )
            )
          ),
          hr(),
          fluidRow(
            column(
              width = 12,
              align = "left",
              fluidRow(
                div(
                  class = "nj-label-control-col",
                  column(
                    width = 12,
                    align = "left",
                    h4(p("Legend"), style = "color:white; position: relative; top: 0px; margin-bottom: -10px; right: -15px")
                  )
                )
              ),
              fluidRow(
                column(
                  width = 8,
                  div(
                    class = "mst-legend-ori",
                    selectInput(
                      "mst_legend_ori",
                      label = "",
                      width = "90%",
                      choices = c("Left" = "left", "Right" = "right"),
                      selected = isolate(mst_legend_ori_reactive())
                    )
                  )
                ),
                column(2),
                column(
                  width = 3,
                  align = "right",
                  dropMenu(
                    actionBttn(
                      "mst_legend_menu",
                      label = "",
                      color = "default",
                      size = "sm",
                      style = "material-flat",
                      icon = icon("sliders")
                    ),
                    placement = "top-start",
                    theme = "translucent",
                    fluidRow(
                      column(
                        width = 11,
                        sliderInput(
                          "mst_font_size",
                          label = h5("Font Size", style = "color:white; margin-bottom: 0px;"),
                          value = isolate(mst_font_size_reactive()),
                          min = 15,
                          max = 30,
                          step = 1,
                          ticks = FALSE,
                          width = "180px"
                        )
                      ),
                      column(1)
                    ),
                    br(),
                    fluidRow(
                      column(
                        width = 11,
                        sliderInput(
                          "mst_symbol_size",
                          label = h5("Key Size", style = "color:white; margin-bottom: 0px;"),
                          value = isolate(mst_symbol_size_reactive()),
                          min = 10,
                          max = 30,
                          step = 1,
                          ticks = FALSE,
                          width = "180px"
                        )
                      ),
                      column(1)
                    )
                  )
                )
              )
            )
          )
        )
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  ##### Export Menu ----
  
  observeEvent(input$mst_download_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    session$sendCustomMessage('mst_reset_style', "")
    session$sendCustomMessage('mst_highlight', "mst_download_menu")
    
    output$mst_controls <- renderUI(
      div(
        class = "control-box",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Export",
          fluidRow(
            column(
              width = 12,
              align = "center",
              br(),
              fluidRow(
                br(),
                column(
                  width = 6,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; left: 10px;',
                                'Save plot as')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  div(
                    class = "filetype-mst",
                    selectInput(
                      inputId = "mst_plot_format",
                      label = "",
                      choices = c("html", "jpeg", "png", "bmp")
                    )
                  )
                )
              ),
              fluidRow(
                column(6),
                column(
                  width = 6,
                  conditionalPanel(
                    "input.mst_plot_format=='jpeg'",
                    actionBttn(
                      "save_plot_jpeg",
                      style = "simple",
                      label = "",
                      size = "sm",
                      icon =  icon("download"),
                      color = "primary"
                    )  
                  ),
                  conditionalPanel(
                    "input.mst_plot_format=='png'",
                    actionBttn(
                      "save_plot_png",
                      style = "simple",
                      label = "",
                      size = "sm",
                      icon =  icon("download"),
                      color = "primary"
                    )
                  ),
                  conditionalPanel(
                    "input.mst_plot_format=='bmp'",
                    actionBttn(
                      "save_plot_bmp",
                      style = "simple",
                      label = "",
                      size = "sm",
                      icon =  icon("download"),
                      color = "primary"
                    )  
                  ),
                  conditionalPanel(
                    "input.mst_plot_format=='html'",
                    downloadBttn(
                      "save_plot_html",
                      style = "simple",
                      label = "",
                      size = "sm",
                      icon =  icon("download"),
                      color = "primary"
                    )
                  )    
                )
              ),
              hr(), 
              fluidRow(
                column(
                  width = 6,
                  align = "left",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 17px',
                                'Print Report')
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "center",
                  actionButton(
                    "create_rep",
                    "",
                    icon = icon("file-waveform")
                  )
                )
              ),
              br(), br()
            ) 
          )
        )
      )
    ) 
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  
  ##### Miscellaneous ----
  
  output$mst_node_shape <- renderUI({
    if(isTRUE(mst_color_var_reactive())) {
      choices <- c("Pie Nodes" = "custom")
      selected <- "custom"
    } else {
      choices <- list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
                     `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon", "Dot" = "dot", "Square" = "square"))
      selected <- mst_node_shape_reactive()
    }
    
    selectInput(
      "mst_node_shape",
      "",
      choices = choices,
      selected = selected
    )
  })
  
  # Reset all control inputs
  observeEvent(input$mst_reset, {
    showModal(
      div(
        class = "load-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    'Resetting all plot control inputs will lead to loss of all current settings. Continue?',
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Reset Plot Settings",
          footer = tagList(
            modalButton("Cancel"),
            actionButton("mst_reset_confirm", "Reset", class = "btn btn-default")
          )
        )
      )
    )
  })
  
  observeEvent(input$mst_reset_confirm, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    removeModal()
    
    mst_node_label_reactive("Assembly Name")
    mst_title_reactive("")
    mst_subtitle_reactive("")
    mst_color_var_reactive(FALSE)
    mst_col_var_reactive("Isolation Date")
    mst_col_scale_reactive("Viridis")
    mst_text_color_reactive("#000000")
    mst_color_node_reactive("#B2FACA")
    mst_color_edge_reactive("#000000")
    mst_edge_font_color_reactive("#000000")
    mst_background_color_reactive("#ffffff")
    mst_background_transparent_reactive(FALSE)
    mst_scale_nodes_reactive(TRUE)
    mst_node_scale_reactive(c(20, 40))
    mst_node_size_reactive(30)
    mst_scale_edges_reactive(TRUE)
    mst_edge_length_scale_reactive(15)
    mst_edge_length_reactive(35)
    mst_edge_font_size_reactive(18)
    mst_node_label_fontsize_reactive(14)
    mst_title_size_reactive(35)
    mst_subtitle_size_reactive(20)
    mst_ratio_reactive(16/10)
    mst_scale_reactive(600)
    mst_shadow_reactive(TRUE)
    mst_node_shape_reactive("dot")
    mst_show_clusters_reactive(FALSE)
    mst_cluster_col_scale_reactive("Viridis")
    mst_cluster_type_reactive("Area")
    mst_cluster_width_reactive(24)
    ifelse(!is.null(DB$cluster_thresh),
           mst_cluster_threshold_reactive(DB$cluster_thresh),
           mst_cluster_threshold_reactive(10))
    mst_legend_ori_reactive("left")
    mst_font_size_reactive(18)
    mst_symbol_size_reactive(20)
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Size scaling MST
  observe({
    if(mst_ratio_reactive() == "1.6") {
      updateSliderInput(session, "mst_scale",
                        step = 5, value = 600, min = 450, max = 670)
    } else if(mst_ratio_reactive() == "1.77777777777778") {
      updateSliderInput(session, "mst_scale",
                        step = 9, value = 657, min = 450, max = 666)
    } else if(mst_ratio_reactive() == "1.33333333333333"){
      updateSliderInput(session, "mst_scale",
                        step = 3, value = 654, min = 450, max = 669)
    }
  })
  
  # Clustering UI
  output$mst_cluster <- renderUI({
    req(DB$schemeinfo)
    
    div(
      class = "mst-threshold",
      numericInput(
        inputId = "mst_cluster_threshold",
        label = NULL,
        value = mst_cluster_threshold_reactive(),
        min = 1,
        max = 99
      )
    )
  })
  
  # MST color mapping
  output$mst_color_mapping <- renderUI({
    mst_color_node <- colorPickr(
      inputId = "mst_color_node",
      width = "100%",
      selected = mst_color_node_reactive(),
      label = "",
      update = "changestop",
      interaction = list(clear = FALSE,
                         save = FALSE),
      position = "right-start"
    )
    
    if(isFALSE(mst_color_var_reactive())) {
      mst_color_node
    } else {
      shinyjs::disabled(mst_color_node)
    }
  })
  
  observeEvent(input$mst_color_var, {
    
    if(isTRUE(input$mst_color_var)) {
      updateSelectizeInput(session, inputId = "mst_node_shape", choices = c("Pie Nodes" = "custom"))
      updateSelectizeInput(session, inputId = "mst_node_label", choices = c("Assembly Name"))
    } else {
      updateSelectizeInput(session, inputId = "mst_node_shape", 
                           choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
                                          `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
                           selected = c("Dot" = "dot"))
      updateSelectizeInput(session, inputId = "mst_node_label",
                           choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
                           selected = "Assembly Name")
    }
  })
  
  # MST node labels 
  output$mst_node_label <- renderUI({
    
    if(isTRUE(mst_color_var_reactive())) {
      choices <- "Assembly Name"
    } else {
      choices <- names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)]
    }
    
    selectInput(
      "mst_node_label",
      label = "",
      choices = choices,
      selected = mst_node_label_reactive(),
      width = "100%"
    )
  })
  
  ### Plot Function ----
  
  #### MST ----
  
  mst_tree <- reactive({
    
    data <- toVisNetworkData(Vis$mst_pre)
    data$nodes <- mutate(data$nodes, 
                         label = Vis$unique_meta[, colnames(Vis$unique_meta) %in% mst_node_label_reactive()],
                         value = mst_node_scaling())
    
    ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
                            var pieData = JSON.parse(metadata);
                            var radius = style.size;
                            var centerX = x;
                            var centerY = y;
                            var total = pieData.reduce((sum, slice) => sum + slice.value, 0)
                            var startAngle = 0;

                            const drawNode = () => {
                                // Set shadow properties
                                if (style.shadow) {
                                  var shadowSize = style.shadowSize;
                                  ctx.shadowColor = style.shadowColor;
                                  ctx.shadowBlur = style.shadowSize;
                                  ctx.shadowOffsetX = style.shadowX;
                                  ctx.shadowOffsetY = style.shadowY;
                                  
                                  ctx.beginPath();
                                  ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
                                  ctx.fill();
                                  
                                  ctx.shadowColor = 'transparent';
                                  ctx.shadowBlur = 0;
                                  ctx.shadowOffsetX = 0;
                                  ctx.shadowOffsetY = 0;
                                }

                                pieData.forEach(slice => {
                                    var sliceAngle = 2 * Math.PI * (slice.value / total);
                                    ctx.beginPath();
                                    ctx.moveTo(centerX, centerY);
                                    ctx.arc(centerX, centerY, radius, startAngle, startAngle + sliceAngle);
                                    ctx.closePath();
                                    ctx.fillStyle = slice.color;
                                    ctx.fill();
                                     if (pieData.length > 1) {
                ctx.strokeStyle = 'black';
                ctx.lineWidth = 1;
                ctx.stroke();
            }
                                    startAngle += sliceAngle;
                                });
                    
                                // Draw a border
                                ctx.beginPath();
                                ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
                                ctx.strokeStyle = 'black';
                                ctx.lineWidth = 1;
                                ctx.stroke();
                            };
                            drawLabel = () => {
                              //Draw the label
                              var lines = label.split(`\n`);
                              var lineHeight = font.size;
                              ctx.font = `${font.size}px ${font.face}`;
                              ctx.fillStyle = font.color;
                              ctx.textAlign = 'center';
                              ctx.textBaseline = 'middle';
                              lines.forEach((line, index) => {
                                ctx.fillText(line, centerX, 
                                centerY + radius + (index + 1) * lineHeight);
                              })
                            }
                            
                            return {
                                drawNode,
                                drawExternalLabel: drawLabel,
                                nodeDimensions: { width: 2 * radius, height: 2 * radius },
                            };
                        }")
    
    Vis$var_cols <- NULL
    
    # Generate pie charts as nodes
    if(isTRUE(mst_color_var_reactive())) {
      
      group <- character(nrow(data$nodes))
      for (i in 1:length(unique(Vis$meta_mst[[mst_col_var_reactive()]]))) {
        group[i] <- unique(Vis$meta_mst[[mst_col_var_reactive()]])[i]
      }
      
      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
      
      if(length(which(data$nodes$group == "")) != 0) {
        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
      }
      
      if(is.null(mst_col_scale_reactive())) {
        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[mst_col_var_reactive()]]),
                                   color = viridis(length(unique(Vis$meta_mst[[mst_col_var_reactive()]]))))
      } else if (mst_col_scale_reactive() == "Rainbow") {
        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[mst_col_var_reactive()]]),
                                   color = rainbow(length(unique(Vis$meta_mst[[mst_col_var_reactive()]]))))
      } else if (mst_col_scale_reactive() == "Viridis") {
        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[mst_col_var_reactive()]]),
                                   color = viridis(length(unique(Vis$meta_mst[[mst_col_var_reactive()]]))))
      }
      
      for(i in 1:nrow(data$nodes)) {
        
        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
        variable <- Vis$meta_mst[[mst_col_var_reactive()]]
        values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
        
        for(j in 1:length(unique(values))) {
          
          share <- sum(unique(values)[j] == values) / length(values) * 100
          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
          
          if(j == 1) {
            pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
          } else {
            pie_vec <- paste0(pie_vec, ',{"value":', share,',"color":"', color,'"}')
          }
        }
        
        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
      }
    }
    
    data$edges <- mutate(data$edges,
                         length = if(isFALSE(mst_scale_edges_reactive())) {
                           mst_edge_length_reactive()
                         } else {
                           log(data$edges$weight) * mst_edge_length_scale_reactive()
                         },
                         label = as.character(data$edges$weight))
    
    if(isTRUE(mst_show_clusters_reactive())) {
      clusters <- compute_clusters(data$nodes, data$edges, mst_cluster_threshold_reactive())
      if(mst_cluster_type_reactive() == "Area") {
        data$nodes$group <- clusters$group
      }
    }
    
    visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                   main = mst_title(),
                                   background = mst_background_color(),
                                   submain = mst_subtitle()) %>%
      visNodes(size = mst_node_size_reactive(),
               shape = mst_node_shape(),
               shadow = mst_shadow_reactive(),
               color = mst_color_node_reactive(),
               ctxRenderer = ctxRendererJS,
               scaling = list(min = mst_node_scale_reactive()[1],
                              max = mst_node_scale_reactive()[2]),
               font = list(color = mst_text_color_reactive(),
                           size = mst_node_label_fontsize_reactive())) %>%
      visEdges(color = mst_color_edge_reactive(),
               font = list(color = mst_edge_font_color_reactive(),
                           size = mst_edge_font_size_reactive(),
                           strokeWidth = 4,
                           strokeColor = mst_background_color())) %>%
      visOptions(collapse = TRUE) %>%
      visInteraction(hover = TRUE) %>%
      visLayout(randomSeed = 1) %>%
      visLegend(useGroups = FALSE,
                zoom = TRUE,
                width = 0.2,
                position = mst_legend_ori_reactive(),
                ncol = legend_col(),
                addNodes = mst_legend())
    
    if(isTRUE(mst_show_clusters_reactive())) {
      no_color <- length(unique(data$nodes$group[duplicated(data$nodes$group)]))
      no_color_edges <- length(unique(clusters$edge_group))
      
      if(mst_cluster_col_scale_reactive() == "Viridis") {
        color_palette <- viridis(no_color)
        color_edges <- viridis(no_color_edges)
      } else {
        color_palette <- rainbow(no_color + 1)
        color_edges <- rainbow(no_color_edges)
      }
      
      j <- 1
      if(mst_cluster_type_reactive() == "Area") {
        for(i in 1:length(unique(data$nodes$group))) {
          # Color only cluster with 2 or more nodes
          if(sum(data$nodes$group == unique(data$nodes$group)[i]) > 1) { 
            visNetwork_graph <- visNetwork_graph %>% 
              visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[j])
            j <- j + 1
          } else {
            visNetwork_graph <- visNetwork_graph %>% 
              visGroups(groupname = unique(data$nodes$group)[i], color = mst_color_node_reactive())
          }
        }
      } else {
        thin_edges <- data$edges
        thin_edges$width <- 2
        thin_edges$color <- "black"
        
        thick_edges <- data$edges
        thick_edges$width <- mst_cluster_width_reactive()
        thick_edges$color <- rep("rgba(0, 0, 0, 0)", length(data$edges$from))
        
        for(i in 1:length(unique(clusters$edge_group))) {
          if(unique(clusters$edge_group)[i] != "0") {
            edge_color <- paste(col2rgb(color_edges[i]), collapse=", ")
            thick_edges$color[clusters$edge_group == unique(clusters$edge_group)[i]] <- paste0("rgba(", edge_color, ", 0.5)")
          }
        }
        merged_edges <- rbind(thick_edges, thin_edges)
        data$edges <- merged_edges
        visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                       main = mst_title(),
                                       background = mst_background_color(),
                                       submain = mst_subtitle()) %>%
          visNodes(size = mst_node_size_reactive(),
                   shape = mst_node_shape(),
                   shadow = mst_shadow_reactive(),
                   color = mst_color_node_reactive(),
                   ctxRenderer = ctxRendererJS,
                   scaling = list(min = mst_node_scale_reactive()[1],
                                  max = mst_node_scale_reactive()[2]),
                   font = list(color = mst_text_color_reactive(),
                               size = mst_node_label_fontsize_reactive())) %>%
          visEdges(color = mst_color_edge_reactive(),
                   font = list(color = mst_edge_font_color_reactive(),
                               size = mst_edge_font_size_reactive(),
                               strokeWidth = 4),
                   smooth = FALSE,
                   physics = FALSE) %>%
          visOptions(collapse = TRUE) %>%
          visInteraction(hover = TRUE) %>%
          visLayout(randomSeed = 1) %>%
          visLegend(useGroups = FALSE,
                    zoom = TRUE,
                    width = 0.2,
                    position = mst_legend_ori_reactive(),
                    ncol = legend_col(),
                    addNodes = mst_legend())
      }
    }
    visNetwork_graph
  })
  
  # MST legend
  legend_col <- reactive({
    if(!is.null(Vis$var_cols)) {
      if(nrow(Vis$var_cols) > 10) {
        3
      } else if(nrow(Vis$var_cols) > 5) {
        2
      } else {
        1
      }
    } else {1}
  })
  
  mst_legend <- reactive({
    if(is.null(Vis$var_cols)) {
      NULL
    } else {
      legend <- Vis$var_cols
      names(legend)[1] <- "label"
      mutate(legend, shape = "dot",
             font.color = mst_text_color_reactive(),
             size = mst_symbol_size_reactive(),
             font.size = mst_font_size_reactive())
    }
  })
  
  # Set MST node shape
  mst_node_shape <- reactive({
    if(mst_node_shape_reactive() == "custom"){
      mst_node_shape_reactive()
    } else if(mst_node_shape_reactive() %in% c("circle", "database", "box", "text")) {
      shinyjs::disable('mst_scale_nodes') 
      updateCheckboxInput(session, "mst_scale_nodes", value = FALSE)
      shinyjs::disable('mst_node_size') 
      shinyjs::disable('mst_node_scale')
      mst_node_shape_reactive()
    } else {
      shinyjs::enable('mst_scale_nodes') 
      shinyjs::enable('mst_node_size') 
      shinyjs::enable('mst_node_scale')
      mst_node_shape_reactive()
    }
  })
  
  # Node Size Scaling
  mst_node_scaling <- reactive({
    if(isTRUE(mst_scale_nodes_reactive())){
      Vis$unique_meta$size
    } else {NULL}
  })
  
  # Set Title
  mst_title <- reactive({
    if(nchar(mst_title_reactive()) < 1) {
      list(text = "title",
           style = paste0(
             "font-family:Georgia, Times New Roman, Times, serif;",
             "text-align:center;",
             "font-size: ", as.character(mst_title_size_reactive()), "px", 
             "; color: ", as.character(mst_background_color()))
      )
    } else {
      list(text = mst_title_reactive(),
           style = paste0(
             "font-family:Georgia, Times New Roman, Times, serif;",
             "text-align:center;",
             "font-size: ", as.character(mst_title_size_reactive()), "px", 
             "; color: ", as.character(mst_text_color_reactive()))
      )
    }
  })
  
  # Set Subtitle
  mst_subtitle <- reactive({
    list(text = mst_subtitle_reactive(),
         style = paste0(
           "font-family:Georgia, Times New Roman, Times, serif;",
           "text-align:center;",
           "font-size: ", as.character(mst_subtitle_size_reactive()), "px", 
           "; color: ", as.character(mst_text_color_reactive()))
    )
  })
  
  # Background color
  
  mst_background_color <- reactive({
    if(isTRUE(mst_background_transparent_reactive())) {
      'rgba(0, 0, 0, 0)'
    } else{
      mst_background_color_reactive()
    }
  })
  
  
  #### Hierarchical Tree ----
  
  make.tree <- reactive({
    
    Vis$nj$tip.label <- Vis$meta_nj$Index
    
    # Convert negative edges 
    edge_lengths_abs <- abs(Vis$nj[["edge.length"]])
    edge_lengths_log <- log(edge_lengths_abs + sqrt(edge_lengths_abs^2 + 1))
    
    Vis_nj <- Vis$nj
    Vis_nj[["edge.length"]] <- edge_lengths_log
    
    if(isTRUE(nj_nodelabel_show_val())) {
      ggtree(
        Vis_nj, alpha = 0.2, layout = layout_nj()) + 
        geom_nodelab(aes(label = node), color = "#29303A", 
                     size = nj_tiplab_size_val() + 1, hjust = 0.7) +
        nj_limit() +
        nj_inward() 
    } else {
      tree <- ggtree(
        Vis_nj, color = nj_color_val(), layout = layout_nj(), 
        ladderize = nj_ladder_val()) %<+% 
        Vis$meta_nj +
        nj_clades() +
        nj_tiplab() +
        nj_tiplab_scale() +
        new_scale_color() +
        nj_limit() +
        nj_inward() +
        nj_label_branch() +
        nj_treescale() +
        nj_nodepoint() +
        nj_tippoint() +
        nj_tippoint_scale() +
        new_scale_color() +
        nj_clip_label() +
        nj_rootedge() +
        ggtitle(label = nj_title_val(),
                subtitle = nj_subtitle_val()) +
        theme_tree(bgcolor = nj_bg_val()) +
        theme(plot.title = element_text(colour = nj_title_color_val(),
                                        size = nj_title_size_val()),
              plot.subtitle = element_text(colour = nj_title_color_val(),
                                           size = nj_subtitle_size_val()),
              legend.background = element_rect(fill = "transparent", 
                                               colour = NA),
              legend.direction = nj_legend_orientation_val(),
              legend.title = element_text(color = nj_color_val(),
                                          size = nj_legend_size_val() * 1.2),
              legend.title.align = 0.5,
              legend.position = c(nj_legend_x_val(), nj_legend_y_val()),
              legend.text = element_text(color = nj_color_val(),
                                         size = nj_legend_size_val()),
              legend.key = element_rect(fill = nj_bg_val()),
              legend.box.spacing = unit(1.5, "cm"),
              legend.key.size = unit(0.05 * nj_legend_size_val(), 'cm'),
              plot.background = element_rect(fill = nj_bg_val(), 
                                             color = nj_bg_val())) +
        new_scale_fill() +
        nj_fruit() +
        nj_gradient() +
        new_scale_fill() +
        nj_fruit2() +
        nj_gradient2() +
        new_scale_fill() +
        nj_fruit3() +
        nj_gradient3() +
        new_scale_fill() +
        nj_fruit4() +
        nj_gradient4() +
        new_scale_fill() +
        nj_fruit5() +
        nj_gradient5() +
        new_scale_fill()

      # Add custom labels
      if(length(Vis$custom_label_nj) > 0) {
        for(i in Vis$custom_label_nj[,1]) {
          ifelse(!is.null(Vis$nj_label_pos_x[[i]]),
                 x_pos <- Vis$nj_label_pos_x[[i]],
                 x_pos <- round(Vis$nj_max_x / 2, 0))

          ifelse(!is.null(Vis$nj_label_pos_y[[i]]),
                 y_pos <- Vis$nj_label_pos_y[[i]],
                 y_pos <- sum(DB$data$Include) / 2)

          ifelse(!is.null(Vis$nj_label_size[[i]]),
                 size <- Vis$nj_label_size[[i]],
                 size <- 5)

          tree <- tree + annotate("text", x = x_pos, y = y_pos, 
                                  label = i, size = size)
        }
      }
      
      # Add heatmap
      if(!is.null(Vis$nj_heatmap_select)) {
        if(isTRUE(nj_heatmap_show_val()) & length(Vis$nj_heatmap_select) > 0) {
          if(!(any(sapply(Vis$meta_nj[Vis$nj_heatmap_select], is.numeric)) &
                any(!sapply(Vis$meta_nj[Vis$nj_heatmap_select], is.numeric)))) {
            tree <- gheatmap.mod(
              tree,
              data = select(Vis$meta_nj, Vis$nj_heatmap_select),
              offset = nj_heatmap_offset_val(),
              width = nj_heatmap_width(),
              legend_title = nj_heatmap_title_val(),
              colnames_angle = -nj_colnames_angle(),
              colnames_offset_y = nj_colnames_y(),
              colnames_color = nj_color_val()) +
              nj_heatmap_scale()
          }
        }
      }
      
      # Sizing control
      Vis$nj_plot <- ggplotify::as.ggplot(tree,
                                          scale = nj_zoom_val(),
                                          hjust = nj_h_val(),
                                          vjust = nj_v_val())

      Vis$nj_true <- TRUE

      # Correct background color if zoomed out
      cowplot::ggdraw(Vis$nj_plot) +
        theme(plot.background = element_rect(fill = nj_bg_val(), 
                                             color = nj_bg_val()))
    }
  })
  
  # Heatmap width
  nj_heatmap_width <- reactive({
    if(!is.null(nj_heatmap_width_val())) {
      nj_heatmap_width_val()
    } else {
      if(!is.null(Vis$nj_heatmap_select)) {
        length_input <- length(Vis$nj_heatmap_select)
        if(nj_layout_val() != "circular" & 
           nj_layout_val() != "inward") {
          if(length_input < 3) {
            0.1
          } else {
            if (length_input >= 3 && length_input <= 50) {
              min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
            } else {
              1.5
            }   
          }
        } else {
          if(length_input < 3) {
            0.3
          } else if (length_input >= 3 && length_input <= 27) {
            min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
          } else {
            3
          }
        }
      } else {NULL}
    }
  })
  
  # Heatmap column titles position
  nj_colnames_y <- reactive({
    if(!is.null(nj_colnames_y_val())) {
      nj_colnames_y_val()
    } else {
      if(nj_layout_val() == "inward" | 
         nj_layout_val() == "circular") {
        0
      } else {-1}
    }
  })
  
  # Heatmap column titles angle
  nj_colnames_angle <- reactive({
    if(!is.null(nj_colnames_angle_val())) {
      nj_colnames_angle_val()
    } else {
      if(nj_layout_val() == "inward" | 
         nj_layout_val() == "circular") {
        90
      } else {-90}
    }
  })
  
  # Heatmap scale
  nj_heatmap_scale <- reactive({
    req(Vis$meta_nj, Vis$nj_heatmap_select)
    
    selected_var <- Vis$meta_nj[Vis$nj_heatmap_select]
    
    if(!(any(sapply(selected_var, is.numeric)) & 
         any(!sapply(selected_var, is.numeric)))) {
      if(any(sapply(selected_var, is.numeric)) |
         length(unique(unlist(selected_var))) > 7) {
        if(nj_heatmap_scale_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                              "RdGy", "RdBu", "PuOr", "PRGn", 
                                              "PiYG", "BrBG")) {
          
          if(nj_heatmap_div_mid_val() == "Zero") {
            midpoint <- 0
          } else if(nj_heatmap_div_mid_val() == "Mean") {
            midpoint <- mean(as.matrix(selected_var), 
                             na.rm = TRUE)
          } else {
            midpoint <- median(as.matrix(selected_var), 
                               na.rm = TRUE)
          }
          scale_fill_gradient2(name = nj_heatmap_title_val(), 
                               low = brewer.pal(3, nj_heatmap_scale_val())[1],
                               mid = brewer.pal(3, nj_heatmap_scale_val())[2],
                               high = brewer.pal(3, nj_heatmap_scale_val())[3],
                               midpoint = midpoint) 
        } else {
          ifelse(any(sapply(selected_var, is.numeric)),
                 discrete <- FALSE,
                 discrete <- TRUE)
          
          if(nj_heatmap_scale_val() == "magma") option <- "A"
          else if(nj_heatmap_scale_val() == "inferno") option <- "B"
          else if(nj_heatmap_scale_val() == "plasma") option <- "C"
          else if(nj_heatmap_scale_val() == "viridis") option <- "D"
          else if(nj_heatmap_scale_val() == "cividis") option <- "E"
          else if(nj_heatmap_scale_val() == "rocket") option <- "F"
          else if(nj_heatmap_scale_val() == "mako") option <- "G"
          else if(nj_heatmap_scale_val() == "turbo") option <- "H"
          else option <- "D"
          
          scale_fill_viridis(name = nj_heatmap_title_val(), 
                             discrete = discrete, option = option)
        }
      } else {
        scale_fill_brewer(name = nj_heatmap_title_val(),
                          palette = nj_heatmap_scale_val())
      } 
    }
  })
  
  # Tippoint Scale
  nj_tippoint_scale <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_tipcolor_mapping_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tippoint_scale_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                           "RdGy", "RdBu", "PuOr", "PRGn", 
                                           "PiYG", "BrBG")) {
        
        if(nj_tipcolor_mapping_div_mid_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tipcolor_mapping_div_mid_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_color_gradient2(name = nj_tipcolor_mapping_val(), 
                              low = brewer.pal(3, nj_tippoint_scale_val())[1],
                              mid = brewer.pal(3, nj_tippoint_scale_val())[2],
                              high = brewer.pal(3, nj_tippoint_scale_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tippoint_scale_val() == "magma") option <- "A"
        else if(nj_tippoint_scale_val() == "inferno") option <- "B"
        else if(nj_tippoint_scale_val() == "plasma") option <- "C"
        else if(nj_tippoint_scale_val() == "viridis") option <- "D"
        else if(nj_tippoint_scale_val() == "cividis") option <- "E"
        else if(nj_tippoint_scale_val() == "rocket") option <- "F"
        else if(nj_tippoint_scale_val() == "mako") option <- "G"
        else if(nj_tippoint_scale_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_color_viridis(name = nj_tipcolor_mapping_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_color_brewer(name = nj_tipcolor_mapping_val(),
                         palette = nj_tippoint_scale_val())
    }
  })
  
  # Tiplab Scale
  nj_tiplab_scale <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_color_mapping_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiplab_scale_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                           "RdGy", "RdBu", "PuOr", "PRGn", 
                                           "PiYG", "BrBG")) {
        
        if(nj_color_mapping_div_mid_val() == "Zero") {
          midpoint <- 0
        } else if(nj_color_mapping_div_mid_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_color_gradient2(name = nj_color_mapping_val(), 
                              low = brewer.pal(3, nj_tiplab_scale_val())[1],
                              mid = brewer.pal(3, nj_tiplab_scale_val())[2],
                              high = brewer.pal(3, nj_tiplab_scale_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiplab_scale_val() == "magma") option <- "A"
        else if(nj_tiplab_scale_val() == "inferno") option <- "B"
        else if(nj_tiplab_scale_val() == "plasma") option <- "C"
        else if(nj_tiplab_scale_val() == "viridis") option <- "D"
        else if(nj_tiplab_scale_val() == "cividis") option <- "E"
        else if(nj_tiplab_scale_val() == "rocket") option <- "F"
        else if(nj_tiplab_scale_val() == "mako") option <- "G"
        else if(nj_tiplab_scale_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_color_viridis(name = nj_color_mapping_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_color_brewer(name = nj_color_mapping_val(),
                         palette = nj_tiplab_scale_val())
    }
  })
  
  # Clade Highlight
  nj_clades <- reactive({
    
    selected_nodes <- nj_parentnode_val()
    if (length(selected_nodes) == 1 && selected_nodes == "") selected_nodes <- NULL
    
    num_clades <- length(selected_nodes)
    
    if(num_clades != 0) {
      if(num_clades > 9) {
        show_toast(
          title = "Max. 9 clade highlights allowed",
          type = "error",
          position = "bottom-end",
          timer = 6000
        )
        return(NULL)
      } else {
        if(!is.null(nj_clade_scale_val())) {
          nj_clade_scale <- nj_clade_scale_val()
        } else {
          if(num_clades == 1) {
            nj_clade_scale <- "#D0F221"
          } else {
            nj_clade_scale <- "Set1"
          }
        }
        
        if(!is.null(nj_clade_type_val())) {
          nj_clade_type <- nj_clade_type_val()
        } else {
          nj_clade_type <- "roundrect"
        }
        
        if(num_clades == 1) {
          if(!startsWith(nj_clade_scale, "#")) {
            fill <- "#D0F221"
          } else {
            fill <- nj_clade_scale
          }
        } else if (num_clades >= 1) {
          ifelse(num_clades < 3, 
                 num_cols <- 3,
                 num_cols <- num_clades)
          
          if(startsWith(nj_clade_scale, "#")) {
            fill <- brewer.pal(num_cols, "Set1")[1:num_clades]
          } else {
            fill <- brewer.pal(num_cols, nj_clade_scale)[1:num_clades]
          }
        }
        
        geom_hilight(node = as.numeric(selected_nodes),
                     fill = fill,
                     type = nj_clade_type,
                     to.bottom = TRUE)
      }
    } else {NULL} 
  })
  
  # Tiles fill fill gradient
  nj_gradient <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_fruit_variable_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiles_scale_1_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                           "RdGy", "RdBu", "PuOr", "PRGn", 
                                           "PiYG", "BrBG")) {
        
        if(nj_tiles_mapping_div_mid_1_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tiles_mapping_div_mid_1_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_fill_gradient2(name = nj_fruit_variable_val(), 
                              low = brewer.pal(3, nj_tiles_scale_1_val())[1],
                              mid = brewer.pal(3, nj_tiles_scale_1_val())[2],
                              high = brewer.pal(3, nj_tiles_scale_1_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiles_scale_1_val() == "magma") option <- "A"
        else if(nj_tiles_scale_1_val() == "inferno") option <- "B"
        else if(nj_tiles_scale_1_val() == "plasma") option <- "C"
        else if(nj_tiles_scale_1_val() == "viridis") option <- "D"
        else if(nj_tiles_scale_1_val() == "cividis") option <- "E"
        else if(nj_tiles_scale_1_val() == "rocket") option <- "F"
        else if(nj_tiles_scale_1_val() == "mako") option <- "G"
        else if(nj_tiles_scale_1_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_fill_viridis(name = nj_fruit_variable_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_fill_brewer(name = nj_fruit_variable_val(),
                         palette = nj_tiles_scale_1_val())
    }
  })
  
  nj_gradient2 <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_fruit_variable_2_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiles_scale_2_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                            "RdGy", "RdBu", "PuOr", "PRGn", 
                                            "PiYG", "BrBG")) {
        
        if(nj_tiles_mapping_div_mid_2_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tiles_mapping_div_mid_2_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_fill_gradient2(name = nj_fruit_variable_2_val(), 
                              low = brewer.pal(3, nj_tiles_scale_2_val())[1],
                              mid = brewer.pal(3, nj_tiles_scale_2_val())[2],
                              high = brewer.pal(3, nj_tiles_scale_2_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiles_scale_2_val() == "magma") option <- "A"
        else if(nj_tiles_scale_2_val() == "inferno") option <- "B"
        else if(nj_tiles_scale_2_val() == "plasma") option <- "C"
        else if(nj_tiles_scale_2_val() == "viridis") option <- "D"
        else if(nj_tiles_scale_2_val() == "cividis") option <- "E"
        else if(nj_tiles_scale_2_val() == "rocket") option <- "F"
        else if(nj_tiles_scale_2_val() == "mako") option <- "G"
        else if(nj_tiles_scale_2_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_fill_viridis(name = nj_fruit_variable_2_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_fill_brewer(name = nj_fruit_variable_2_val(),
                         palette = nj_tiles_scale_2_val())
    }
  })
  
  nj_gradient3 <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_fruit_variable_3_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiles_scale_3_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                            "RdGy", "RdBu", "PuOr", "PRGn", 
                                            "PiYG", "BrBG")) {
        
        if(nj_tiles_mapping_div_mid_3_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tiles_mapping_div_mid_3_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_fill_gradient2(name = nj_fruit_variable_3_val(), 
                              low = brewer.pal(3, nj_tiles_scale_3_val())[1],
                              mid = brewer.pal(3, nj_tiles_scale_3_val())[2],
                              high = brewer.pal(3, nj_tiles_scale_3_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiles_scale_3_val() == "magma") option <- "A"
        else if(nj_tiles_scale_3_val() == "inferno") option <- "B"
        else if(nj_tiles_scale_3_val() == "plasma") option <- "C"
        else if(nj_tiles_scale_3_val() == "viridis") option <- "D"
        else if(nj_tiles_scale_3_val() == "cividis") option <- "E"
        else if(nj_tiles_scale_3_val() == "rocket") option <- "F"
        else if(nj_tiles_scale_3_val() == "mako") option <- "G"
        else if(nj_tiles_scale_3_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_fill_viridis(name = nj_fruit_variable_3_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_fill_brewer(name = nj_fruit_variable_3_val(),
                         palette = nj_tiles_scale_3_val())
    }
  })
  
  nj_gradient4 <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_fruit_variable_4_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiles_scale_4_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                            "RdGy", "RdBu", "PuOr", "PRGn", 
                                            "PiYG", "BrBG")) {
        
        if(nj_tiles_mapping_div_mid_4_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tiles_mapping_div_mid_4_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_fill_gradient2(name = nj_fruit_variable_4_val(), 
                              low = brewer.pal(3, nj_tiles_scale_4_val())[1],
                              mid = brewer.pal(3, nj_tiles_scale_4_val())[2],
                              high = brewer.pal(3, nj_tiles_scale_4_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiles_scale_4_val() == "magma") option <- "A"
        else if(nj_tiles_scale_4_val() == "inferno") option <- "B"
        else if(nj_tiles_scale_4_val() == "plasma") option <- "C"
        else if(nj_tiles_scale_4_val() == "viridis") option <- "D"
        else if(nj_tiles_scale_4_val() == "cividis") option <- "E"
        else if(nj_tiles_scale_4_val() == "rocket") option <- "F"
        else if(nj_tiles_scale_4_val() == "mako") option <- "G"
        else if(nj_tiles_scale_4_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_fill_viridis(name = nj_fruit_variable_4_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_fill_brewer(name = nj_fruit_variable_4_val(),
                         palette = nj_tiles_scale_4_val())
    }
  })
  
  nj_gradient5 <- reactive({
    req(Vis$meta_nj)
    
    selected_var <- Vis$meta_nj[nj_fruit_variable_5_val()]
    
    if(class(unlist(selected_var)) == "numeric" |
       length(unique(unlist(selected_var))) > 7) {
      if(nj_tiles_scale_5_val() %in% c("Spectral", "RdYlGn", "RdYlBu", 
                                            "RdGy", "RdBu", "PuOr", "PRGn", 
                                            "PiYG", "BrBG")) {
        
        if(nj_tiles_mapping_div_mid_5_val() == "Zero") {
          midpoint <- 0
        } else if(nj_tiles_mapping_div_mid_5_val() == "Mean") {
          midpoint <- mean(as.matrix(selected_var), 
                           na.rm = TRUE)
        } else {
          midpoint <- median(as.matrix(selected_var), 
                             na.rm = TRUE)
        }
        scale_fill_gradient2(name = nj_fruit_variable_5_val(), 
                              low = brewer.pal(3, nj_tiles_scale_5_val())[1],
                              mid = brewer.pal(3, nj_tiles_scale_5_val())[2],
                              high = brewer.pal(3, nj_tiles_scale_5_val())[3],
                              midpoint = midpoint) 
      } else {
        ifelse(class(unlist(selected_var)) == "numeric",
               discrete <- FALSE,
               discrete <- TRUE)
        
        if(nj_tiles_scale_5_val() == "magma") option <- "A"
        else if(nj_tiles_scale_5_val() == "inferno") option <- "B"
        else if(nj_tiles_scale_5_val() == "plasma") option <- "C"
        else if(nj_tiles_scale_5_val() == "viridis") option <- "D"
        else if(nj_tiles_scale_5_val() == "cividis") option <- "E"
        else if(nj_tiles_scale_5_val() == "rocket") option <- "F"
        else if(nj_tiles_scale_5_val() == "mako") option <- "G"
        else if(nj_tiles_scale_5_val() == "turbo") option <- "H"
        else option <- "D"
        
        scale_fill_viridis(name = nj_fruit_variable_5_val(), 
                            discrete = discrete, option = option)
      }
    } else {
      scale_fill_brewer(name = nj_fruit_variable_5_val(),
                         palette = nj_tiles_scale_5_val())
    }
  })
  
  # No label clip off for linear NJ tree
  nj_clip_label <- reactive({
    if(nj_layout_val() != "circular" &
       nj_layout_val() != "inward") {
      coord_cartesian(clip = "off")
    } else {NULL}
  })
  
  # Geom Fruit
  nj_fruit <- reactive({
    if(isTRUE(nj_tiles_show_1_val())) {
      geom_fruit(
        geom = geom_tile,
        mapping = aes(fill= !!sym(nj_fruit_variable_val())),
        offset = nj_fruit_offset_circ_val(),
        width = nj_fruit_width_circ_val(),
        alpha = nj_fruit_alpha_val()
      )
    } else {NULL}
  })
  
  # Geom Fruit
  nj_fruit2 <- reactive({
    if(isTRUE(nj_tiles_show_2_val())) {
      geom_fruit(
        geom = geom_tile,
        mapping = aes(fill= !!sym(nj_fruit_variable_2_val())),
        offset = nj_fruit_offset_circ_2_val(),
        width = nj_fruit_width_circ_2_val(),
        alpha = nj_fruit_alpha_2_val()
      )
    } else {NULL}
  })
  
  nj_fruit3 <- reactive({
    if(isTRUE(nj_tiles_show_3_val())) {
      geom_fruit(
        geom = geom_tile,
        mapping = aes(fill= !!sym(nj_fruit_variable_3_val())),
        offset = nj_fruit_offset_circ_3_val(),
        width = nj_fruit_width_circ_3_val(),
        alpha = nj_fruit_alpha_3_val()
      )
    } else {NULL}
  })
  
  nj_fruit4 <- reactive({
    if(isTRUE(nj_tiles_show_4_val())) {
      geom_fruit(
        geom = geom_tile,
        mapping = aes(fill= !!sym(nj_fruit_variable_4_val())),
        offset = nj_fruit_offset_circ_4_val(),
        width = nj_fruit_width_circ_4_val(),
        alpha = nj_fruit_alpha_4_val()
      )
    } else {NULL}
  })
  
  nj_fruit5 <- reactive({
    if(isTRUE(nj_tiles_show_5_val())) {
      geom_fruit(
        geom = geom_tile,
        mapping = aes(fill= !!sym(nj_fruit_variable_5_val())),
        offset = nj_fruit_offset_circ_5_val(),
        width = nj_fruit_width_circ_5_val(),
        alpha = nj_fruit_alpha_5_val()
      )
    } else {NULL}
  })
  
  # Xlim
  nj_limit <- reactive({
    if(nj_layout_val() == "circular") {
      xlim(nj_xlim_val(), NA)
    } else {NULL}
  })
  
  # NJ inward circular
  nj_inward <- reactive({
    if(nj_layout_val() == "inward") {
      if(between(nj_xlim_inw_val(), 30, 120)){
        xlim <- nj_xlim_inw_val()
      } else {
        xlim <- 50
      }
      layout_inward_circular(xlim = xlim)
    } else {
      NULL
    }
  })
  
  # Treescale
  nj_treescale <- reactive({
    if(nj_layout_val() != "circular") {
      if(isTRUE(nj_treescale_show_val())) {
        if(nj_treescale_width_val() < 1) {
          width <- 1
        } else { width <- nj_treescale_width_val()}
        geom_treescale(x = nj_treescale_x_val(),
                       y = nj_treescale_y_val(),
                       width = width,
                       color = nj_color_val(),
                       fontsize = 4)
      } else {NULL}
    } else {NULL}
  }) 
  
  # Label branches
  nj_label_branch <- reactive({
    if(nj_layout_val() != "circular" | 
       nj_layout_val() != "inward") {
      if(isTRUE(nj_show_branch_label_val())) {
        geom_label(
          aes(
            x=!!sym("branch"), 
            label= !!sym(nj_branch_label_val())),
          fill = nj_branch_label_color_val(),
          size = nj_branch_size_val(),
          label.r = unit(nj_branch_labelradius_val(), "lines"),
          nudge_x = nj_branch_x_val(),
          fontface = nj_branchlab_fontface_val(),
          alpha = nj_branchlab_alpha_val()
        )
      } else {NULL}
    } else {NULL}
  })
  
  # Rootedge
  nj_rootedge <- reactive({
    if(isTRUE(nj_rootedge_show_val())) {
      geom_rootedge(rootedge = nj_rootedge_length_val(),
                    linetype = nj_rootedge_line_val())
    } else {NULL}
  })
  
  # Tippoints
  nj_tippoint <- reactive({
    if (!isTRUE(nj_tippoint_show_val()) && 
        !isTRUE(nj_tipcolor_mapping_show_val()) && 
        !isTRUE(nj_tipshape_mapping_show_val())) {
      return(NULL)
    }
    
    aes_list <- list()
    
    if(isTRUE(nj_tipcolor_mapping_show_val())) {
      aes_list$color <- sym(nj_tipcolor_mapping_val())
    }
    if(isTRUE(nj_tipshape_mapping_show_val())) {
      aes_list$shape <- sym(nj_tipshape_mapping_val())
    }
    
    args <- list(
      mapping = do.call(aes, aes_list),
      alpha = nj_tippoint_alpha_val(),
      size = nj_tippoint_size_val()
    )
    
    if(!isTRUE(nj_tipcolor_mapping_show_val())) {
      args$color <- nj_tippoint_color_val()
      args$fill <- nj_tippoint_color_val()  
    }
    
    if(!isTRUE(nj_tipshape_mapping_show_val())) {
      args$shape <- nj_tippoint_shape_val()
    }
    
    do.call(geom_tippoint, args)
  })
  
  # Nodepoints
  nj_nodepoint <- reactive({
    if(isTRUE(nj_nodepoint_show_val())) {
      geom_nodepoint(
        alpha = nj_nodepoint_alpha_val(),
        color = nj_nodepoint_color_val(),
        shape = nj_nodepoint_shape_val(),
        size = nj_nodepoint_size_val()
      )
    } else {NULL}
  })
  
  # NJ circularity
  nj_tiplab <- reactive({
    aes <- aes(
      label = !!sym(nj_tiplab_val()),
      color = if(isTRUE(nj_mapping_show_val())) !!sym(nj_color_mapping_val()) else NULL
    )
    
    common_params <- list(
      geom = if(isTRUE(nj_geom_val())) "label" else "text",
      size = nj_tiplab_size_val(),
      alpha = nj_tiplab_alpha_val(),
      fontface = nj_tiplab_fontface_val(),
      align = nj_align_val()
    )
    
    if(nj_layout_val() != "inward" & nj_layout_val() != "circular") {
      common_params$angle <- nj_tiplab_angle_val()
      common_params$nudge_x <- nj_tiplab_position_val()
    } else {
      common_params$hjust <- nj_tiplab_position_val()
    }
    
    if(isTRUE(nj_geom_val())) {
      common_params <- append(common_params, list(
        label.padding = unit(nj_tiplab_padding_val(), "lines"),
        label.r = unit(nj_tiplab_labelradius_val(), "lines"),
        fill = nj_tiplab_fill_val()
      ))
    }
    
    if(!isTRUE(nj_mapping_show_val())) {
      common_params <- append(common_params, 
                              list(color = nj_tiplab_color_val()))
    }
    
    if (isTRUE(nj_tiplab_show_val())) {
      do.call(geom_tiplab, c(list(mapping = aes), 
                             common_params))
    }
  })
  
  # NJ Tree Layout
  layout_nj <- reactive({
    if(nj_layout_val() == "inward") {
      "circular"
    } else {nj_layout_val()}
  })
  
  
  ### Save MST Plot ----
  output$save_plot_html <- downloadHandler(
    filename = function() {
      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
      paste0("MST_", Sys.Date(), ".html")
    },
    content = function(file) {
      mst_tree() %>% visSave(file = file, background = mst_background_color())
    }
  )
  
  ### Save NJ Plot ----
  
  # Define download handler to save the plot
  
  output$download_nj <- downloadHandler(
    filename = function() {
      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
      paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
    },
    content = function(file) {
      if (input$filetype_nj == "png") {
        png(file, width = (as.numeric(nj_scale_val()) * 
                             as.numeric(nj_ratio_val())), 
            height = as.numeric(nj_scale_val()))
        print(make.tree())
        dev.off()
      } else if (input$filetype_nj == "jpeg") {
        jpeg(file, width = (as.numeric(nj_scale_val()) * 
                              as.numeric(nj_ratio_val())), 
             height = as.numeric(nj_scale_val()), quality = 100)
        print(make.tree())
        dev.off()
      } else if (input$filetype_nj == "svg") {
        plot <- print(make.tree())
        ggsave(file=file, plot=plot, device = svg(
          width = (as.numeric(nj_scale_val()) * 
                     as.numeric(nj_ratio_val()))/96,
          height = as.numeric(nj_scale_val())/96))
      } else if (input$filetype_nj == "bmp") {
        bmp(file, width = (as.numeric(nj_scale_val()) * 
                             as.numeric(nj_ratio_val())), 
            height = as.numeric(nj_scale_val()))
        print(make.tree())
        dev.off()
      }
    }
  )
  
  
  ### Reactive Events ----
  
  observeEvent(input$nj_heatmap_confirm, {
    
    if(isFALSE(nj_heatmap_show_val())) {
      nj_heatmap_show_val(TRUE)
      updateSwitchInput(session, "nj_heatmap_show", value = TRUE)
    }
    
    removeModal()
    
    if(input$nj_heatmap_map == "Variables") {
      Vis$nj_heatmap_select <- input$nj_heatmap_select
    } else if(input$nj_heatmap_map == "AMR Profile") {
      if(isTRUE(input$nj_heatmap_cluster)) {
        
        df_numeric <- as.data.frame(lapply(Vis$amr_nj[,input$nj_heatmap_select], as.numeric))
        
        # Compute distance matrix using Jaccard distance 
        dist_matrix <- dist(t(df_numeric), method = "binary")
        
        # Hierarchical clustering
        hc <- hclust(dist_matrix)
        
        # Reorder columns based on clustering
        Vis$nj_heatmap_select <- input$nj_heatmap_select[hc$order]
      } else {
        Vis$nj_heatmap_select <- input$nj_heatmap_select
      }
    }
  })
  
  # MST cluster reset button
  observeEvent(input$mst_cluster_reset, {
    if(!is.null(DB$schemeinfo))
      updateNumericInput(session, "mst_cluster_threshold", value = DB$cluster_thresh)
  })
  
  # Conditional disabling of control elemenmts
  observe({
    req(input$nj_layout)
    
    # Tiles for inward layout
    if(input$nj_layout == "inward") {
      shinyjs::disable('nj_tiles_show') 
      shinyjs::disable('nj_tiles_show_2')
      shinyjs::disable('nj_tiles_show_3') 
      shinyjs::disable('nj_tiles_show_4')
      shinyjs::disable('nj_tiles_show_5') 
      shinyjs::disable('nj_fruit_variable')
      shinyjs::disable('nj_fruit_variable_2')
      shinyjs::disable('nj_fruit_variable_3')
      shinyjs::disable('nj_fruit_variable_4')
      shinyjs::disable('nj_fruit_variable_5')
      shinyjs::disable('nj_fruit_width')
      shinyjs::disable('nj_fruit_width_2')
      shinyjs::disable('nj_fruit_width_3')
      shinyjs::disable('nj_fruit_width_4')
      shinyjs::disable('nj_fruit_width_5')
      shinyjs::disable('nj_fruit_offset')
      shinyjs::disable('nj_fruit_offset_2')
      shinyjs::disable('nj_fruit_offset_3')
      shinyjs::disable('nj_fruit_offset_4')
      shinyjs::disable('nj_fruit_offset_5')
    } else {
      shinyjs::enable('nj_tiles_show') 
      shinyjs::enable('nj_tiles_show_2')
      shinyjs::enable('nj_tiles_show_3') 
      shinyjs::enable('nj_tiles_show_4')
      shinyjs::enable('nj_tiles_show_5') 
      shinyjs::enable('nj_fruit_variable')
      shinyjs::enable('nj_fruit_variable_2')
      shinyjs::enable('nj_fruit_variable_3')
      shinyjs::enable('nj_fruit_variable_4')
      shinyjs::enable('nj_fruit_variable_5')
      shinyjs::enable('nj_fruit_width')
      shinyjs::enable('nj_fruit_width_2')
      shinyjs::enable('nj_fruit_width_3')
      shinyjs::enable('nj_fruit_width_4')
      shinyjs::enable('nj_fruit_width_5')
      shinyjs::enable('nj_fruit_offset')
      shinyjs::enable('nj_fruit_offset_2')
      shinyjs::enable('nj_fruit_offset_3')
      shinyjs::enable('nj_fruit_offset_4')
      shinyjs::enable('nj_fruit_offset_5')
    }
    
    # Shut off branch labels for circular layout
    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
      shinyjs::disable('nj_show_branch_label')
    } else {
      shinyjs::enable('nj_show_branch_label')
    }
  })
  
  #### Make Plot ----
  
  # Get distances
  hamming_dist <- reactive({
    if(anyNA(DB$allelic_profile)) {
      if(input$na_handling == "omit") {
        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
        
        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
        
        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
        
      } else if(input$na_handling == "ignore_na"){
        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
        
      } else {
        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
      } 
      
    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
  })
  
  hamming_mst <- reactive({
    if(anyNA(DB$allelic_profile)) {
      if(input$na_handling == "omit") {
        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
        
        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
        
        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
        
      } else if (input$na_handling == "ignore_na") {
        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
      } else {
        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
      }
    } else {
      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
    }
    
    # Find indices of pairs with a distance of 0
    zero_distance_pairs <- as.data.frame(which(as.matrix(dist) == 0, arr.ind = TRUE))
    
    zero_distance_pairs <- zero_distance_pairs[zero_distance_pairs$row != zero_distance_pairs$col, ]
    
    if(nrow(zero_distance_pairs) > 0) {
      
      # Sort each row so that x <= y
      df_sorted <- t(apply(zero_distance_pairs, 1, function(row) sort(row)))
      
      # Remove duplicate rows
      df_unique <- as.data.frame(unique(df_sorted))
      
      colnames(df_unique) <- c("col", "row")
      
      # get metadata in df
      vector_col <- character(0)
      count <- 1
      for (i in df_unique$col) {
        vector_col[count] <- Vis$meta_mst$`Assembly Name`[i]
        count <- count + 1
      }
      
      vector_row <- character(0)
      count <- 1
      for (i in df_unique$row) {
        vector_row[count] <- Vis$meta_mst$`Assembly Name`[i]
        count <- count + 1
      }
      
      col_id <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_id[count] <- Vis$meta_mst$`Assembly ID`[i]
        count <- count + 1
      }
      
      row_id <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_id[count] <- Vis$meta_mst$`Assembly ID`[i]
        count <- count + 1
      }
      
      col_index <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_index[count] <- Vis$meta_mst$Index[i]
        count <- count + 1
      }
      
      row_index <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_index[count] <- Vis$meta_mst$Index[i]
        count <- count + 1
      }
      
      col_date <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_date[count] <- Vis$meta_mst$`Isolation Date`[i]
        count <- count + 1
      }
      
      row_date <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_date[count] <- Vis$meta_mst$`Isolation Date`[i]
        count <- count + 1
      }
      
      col_host <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_host[count] <- Vis$meta_mst$Host[i]
        count <- count + 1
      }
      
      row_host <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_host[count] <- Vis$meta_mst$Host[i]
        count <- count + 1
      }
      
      col_country <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_country[count] <- Vis$meta_mst$Country[i]
        count <- count + 1
      }
      
      row_country <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_country[count] <- Vis$meta_mst$Country[i]
        count <- count + 1
      }
      
      col_city <- character(0)
      count <- 1
      for (i in df_unique$col) {
        col_city[count] <- Vis$meta_mst$City[i]
        count <- count + 1
      }
      
      row_city <- character(0)
      count <- 1
      for (i in df_unique$row) {
        row_city[count] <- Vis$meta_mst$City[i]
        count <- count + 1
      }
      
      df_unique <- cbind(df_unique, col_name = vector_col, row_name = vector_row, 
                         col_index = col_index, row_index = row_index, col_id = col_id,
                         row_id = row_id, col_date = col_date, row_date = row_date,
                         col_host = col_host, row_host = row_host, col_country = col_country,
                         row_country = row_country, col_city = col_city, row_city = row_city)
      
      # Add groups
      grouped_df <- df_unique %>%
        group_by(col) %>%
        mutate(group_id = cur_group_id())
      
      # Merge groups
      name <- character(0)
      index <- character(0)
      id <- character(0)
      count <- 1
      for (i in grouped_df$group_id) {
        name[count] <- paste(unique(append(grouped_df$col_name[which(grouped_df$group_id == i)], 
                                           grouped_df$row_name[which(grouped_df$group_id == i)])), 
                             collapse = "\n")
        
        id[count] <- paste(unique(append(grouped_df$col_id[which(grouped_df$group_id == i)], 
                                         grouped_df$row_id[which(grouped_df$group_id == i)])), 
                           collapse = "\n")
        
        index[count] <- paste(unique(append(grouped_df$col_index[which(grouped_df$group_id == i)], 
                                            grouped_df$row_index[which(grouped_df$group_id == i)])), 
                              collapse = "\n")
        
        count <- count + 1
      }
      
      merged_names <- cbind(grouped_df, "Index" = index, "Assembly Name" = name, "Assembly ID" = id)
      
      # remove duplicate groups
      
      final <- merged_names[!duplicated(merged_names$group_id), ]
      
      final_cleaned <- final[!(final$col_name %in% final$row_name),]
      
      final_cleaned <- select(final_cleaned, 3, 17:20)
      
      # adapt metadata
      Date_merged <- character(0)
      for(j in 1:length(final_cleaned$Index)) {
        Date <- character(0)
        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
          Date <- append(Date, Vis$meta_mst$`Isolation Date`[which(Vis$meta_mst$Index == i)])
        }
        Date_merged <- append(Date_merged, paste(Date, collapse = "\n"))
      }
      
      Host_merged <- character(0)
      for(j in 1:length(final_cleaned$Index)) {
        Host <- character(0)
        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
          Host <- append(Host, Vis$meta_mst$Host[which(Vis$meta_mst$Index == i)])
        }
        Host_merged <- append(Host_merged, paste(Host, collapse = "\n"))
      }
      
      Country_merged <- character(0)
      for(j in 1:length(final_cleaned$Index)) {
        Country <- character(0)
        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
          Country <- append(Country, Vis$meta_mst$Country[which(Vis$meta_mst$Index == i)])
        }
        Country_merged <- append(Country_merged, paste(Country, collapse = "\n"))
      }
      
      City_merged <- character(0)
      for(j in 1:length(final_cleaned$Index)) {
        City <- character(0)
        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
          City <- append(City, Vis$meta_mst$City[which(Vis$meta_mst$Index == i)])
        }
        City_merged <- append(City_merged, paste(City, collapse = "\n"))
      }
      
      final_meta <- cbind(final_cleaned, "Isolation Date" = Date_merged, 
                          "Host" = Host_merged, "Country" = Country_merged, "City" = City_merged)
      
      
      # Merging with original data frame / allelic profile
      
      allelic_profile_true <- DB$allelic_profile_true
      meta_true <- Vis$meta_mst
      
      rownames(allelic_profile_true) <- Vis$meta_mst$`Assembly Name`
      rownames(meta_true) <- Vis$meta_mst$`Assembly Name`
      
      omit <- unique(append(df_unique$col_name, df_unique$row_name)) %in% final_cleaned$col_name
      
      omit_id <- unique(append(df_unique$col_name, df_unique$row_name))[!omit]
      
      remove <- !(rownames(allelic_profile_true) %in% omit_id)
      
      allelic_profile_clean <- allelic_profile_true[remove, ]
      
      meta_clean <- meta_true[remove, ]
      
      # substitute meta assembly names with group names
      
      count <- 1
      for(i in which(rownames(meta_clean) %in% final_meta$col_name)) {
        meta_clean$Index[i] <- final_meta$Index[count]
        meta_clean$`Assembly Name`[i] <- final_meta$`Assembly Name`[count]
        meta_clean$`Assembly ID`[i] <- final_meta$`Assembly ID`[count]
        meta_clean$`Isolation Date`[i] <- final_meta$`Isolation Date`[count]
        meta_clean$Host[i] <- final_meta$Host[count]
        meta_clean$Country[i] <- final_meta$Country[count]
        meta_clean$City[i] <- final_meta$City[count]
        count <- count + 1
      }
      
      # Metadata completion
      # get group size
      
      size_vector <- numeric(0)
      for(i in 1:nrow(meta_clean)) {
        if (str_count(meta_clean$`Assembly Name`[i], "\n") == 0) {
          size_vector[i] <- 1
        } else {
          size_vector[i] <- str_count(meta_clean$`Assembly Name`[i], "\n") +1
        }
      }
      
      meta_clean <- mutate(meta_clean, size = size_vector)
      
      # get font size dependent on group size
      
      font_size <- numeric(nrow(meta_clean))
      
      for (i in 1:length(font_size)) {
        if(meta_clean$size[i] < 3) {
          font_size[i] <- 12
        } else {
          font_size[i] <- 11
        }
      }
      
      # get v-align dependent on group size
      valign <- numeric(nrow(meta_clean))
      
      for (i in 1:length(valign)) {
        if(meta_clean$size[i] == 1) {
          valign[i] <- -30
        } else if(meta_clean$size[i] == 2) {
          valign[i] <- -38
        } else if(meta_clean$size[i] == 3) {
          valign[i] <- -46
        } else if(meta_clean$size[i] == 4) {
          valign[i] <- -54
        } else if(meta_clean$size[i] == 5) {
          valign[i] <- -62
        } else if(meta_clean$size[i] > 5) {
          valign[i] <- -70
        }
      }
      
      Vis$unique_meta <- meta_clean %>%
        cbind(font_size = font_size, valign = valign)
      
      # final dist calculation
      
      if(anyNA(DB$allelic_profile)){
        if(input$na_handling == "omit") {
          allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
        } else if (input$na_handling == "ignore_na") {
          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
        } else {
          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
        }
      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
      
      
    } else {
      font_size <- rep(12, nrow(Vis$meta_mst))
      valign <- rep(-30, nrow(Vis$meta_mst))
      size <- rep(1, nrow(Vis$meta_mst))
      Vis$unique_meta <- Vis$meta_mst %>%
        cbind(size , font_size, valign)
      
      dist
    }
    
  })
  
  observeEvent(input$create_tree, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Input create_tree")
    
    if(is.null(DB$data)) {
      log_print("Missing data")
      
      show_toast(
        title = "Missing data",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    } else if(nrow(DB$allelic_profile_true) < 3) {
      log_print("Min. of 3 entries required for visualization")
      
      show_toast(
        title = "Min. of 3 entries required for visualization",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      
      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
        log_print("Duplicated assemblies")
        
        dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
        dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
        
        showModal(
          div(
            class = "start-modal",
            modalDialog(
              if((length(dup_name) + length(dup_id)) == 1) {
                if(length(dup_name) == 1) {
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                            "Entry #", dup_name,
                            " contains a duplicated assembly name:", "<br><br>",
                            DB$meta_true$`Assembly Name`[dup_name],
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  )
                } else {
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                            "Entry #", dup_id,
                            " contains a duplicated assembly ID:", "<br><br>",
                            DB$meta_true$`Assembly ID`[dup_id],
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  )
                }
              } else {
                if(length(dup_name) == 0) {
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                            c("Entries contain duplicated IDs <br><br>",
                              paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), 
                                     "<br>")),
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  )
                } else if(length(dup_id) == 0) {
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                            c("Entries contain duplicated names<br><br>",
                              paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")),
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  )
                } else {
                  fluidRow(
                    br(), 
                    column(
                      width = 11,
                      p(
                        HTML(
                          paste0(
                            '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                            c("Entries contain duplicated names and IDs <br><br>",
                              paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
                              paste0("ID: ", unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")),
                            '</span>'
                          )
                        )
                      )
                    ),
                    br()
                  )
                }
              },
              title = "Duplicate entries",
              fade = TRUE,
              easyClose = TRUE,
              footer = tagList(
                modalButton("Cancel"),
                actionButton("change_entries", "Go to Entry Table", class = "btn btn-default")
              )
            )
          )
        )
      } else {
        
        set.seed(1)
        
        if(input$tree_type == "Tree") {
          
          log_print("Rendering tree plot")
          
          output$tree_field <- renderUI({
            addSpinner(
              plotOutput("tree_plot", 
                         width = paste0(
                           as.character(as.numeric(nj_scale_val()) * 
                                          as.numeric(nj_ratio_val())), "px"), 
                         height = paste0(as.character(nj_scale_val()), "px")),
              spin = "dots",
              color = "#ffffff"
            )
          })
          
          meta_nj <- select(DB$meta_true, -2)
          if(file.exists(file.path(Startup$database, 
                                   gsub(" ", "_", DB$scheme),
                                   "AMR_Profile.rds"))) {
            
            amr_profile <- readRDS(file.path(Startup$database, 
                                             gsub(" ", "_", DB$scheme),
                                             "AMR_Profile.rds"))
            
            if(isFALSE(any(meta_nj$Screened != "Yes"))) {
              Vis$amr_nj <- amr_profile$results[rownames(amr_profile$results) %in% meta_nj$`Assembly ID`, ]
              meta_nj <- add_column(meta_nj, Vis$amr_nj)
            } 
          }
          
          if(length(unique(gsub(" ", "_", colnames(meta_nj)))) < length(gsub(" ", "_", colnames(meta_nj)))) {
            show_toast(
              title = "Conflicting Custom Variable Names",
              type = "warning",
              position = "bottom-end",
              timer = 6000
            )
          } else {
            
            # Create phylogenetic tree data
            if(input$tree_algo == "Neighbour-Joining") {
              Vis_nj <- ape::nj(hamming_dist())
              Vis$tree_algo <- "NJ"
            } else {
              Vis_nj <- phangorn::upgma(hamming_dist())
              Vis$tree_algo <- "UPGMA"
            }
            
            edge_lengths_abs <- abs(Vis_nj[["edge.length"]])
            edge_lengths_log <- log(edge_lengths_abs + sqrt(edge_lengths_abs^2 + 1))
            Vis_nj[["edge.length"]] <- edge_lengths_log
            Vis$nj <- Vis_nj
            
            # Create phylogenetic tree meta data
            Vis$meta_nj <- mutate(meta_nj, taxa = Index) %>%
              relocate(taxa)
            
            # Get number of included entries calculate start values for tree 
            if(nj_layout_val() == "circular" | nj_layout_val() == "inward") {
              if(sum(DB$data$Include) < 21) {
                Vis$labelsize_nj <- 5.5
                Vis$tippointsize_nj <- 5.5
                Vis$nodepointsize_nj <- 4
                Vis$tiplab_padding_nj <- 0.25
                Vis$branch_size_nj <- 4.5
              } else if (between(sum(DB$data$Include), 21, 40)) {
                Vis$labelsize_nj <- 5
                Vis$tippointsize_nj <- 5
                Vis$nodepointsize_nj <- 3.5
                Vis$tiplab_padding_nj <- 0.2
                Vis$branch_size_nj <- 4
              } else if (between(sum(DB$data$Include), 41, 60)) {
                Vis$labelsize_nj <- 4.5
                Vis$tippointsize_nj <- 4.5
                Vis$nodepointsize_nj <- 3
                Vis$tiplab_padding_nj <- 0.15
                Vis$branch_size_nj <- 3.5
              } else if (between(sum(DB$data$Include), 61, 80)) {
                Vis$labelsize_nj <- 4
                Vis$tippointsize_nj <- 4
                Vis$nodepointsize_nj <- 2.5
                Vis$tiplab_padding_nj <- 0.1
                Vis$branch_size_nj <- 3
              } else if (between(sum(DB$data$Include), 81, 100)) {
                Vis$labelsize_nj <- 3.5
                Vis$tippointsize_nj <- 3.5
                Vis$nodepointsize_nj <- 2
                Vis$tiplab_padding_nj <- 0.1
                Vis$branch_size_nj <- 2.5
              } else {
                Vis$labelsize_nj <- 3
                Vis$tippointsize_nj <- 3
                Vis$nodepointsize_nj <- 1.5
                Vis$tiplab_padding_nj <- 0.05
                Vis$branch_size_nj <- 2
              }
            } else {
              if(sum(DB$data$Include) < 21) {
                Vis$labelsize_nj <- 5
                Vis$tippointsize_nj <- 5
                Vis$nodepointsize_nj <- 4
                Vis$tiplab_padding_nj <- 0.25
                Vis$branch_size_nj <- 4.5
              } else if (between(sum(DB$data$Include), 21, 40)) {
                Vis$labelsize_nj <- 4.5
                Vis$tippointsize_nj <- 4.5
                Vis$nodepointsize_nj <- 3.5
                Vis$tiplab_padding_nj <- 0.2
                Vis$branch_size_nj <- 4
              } else if (between(sum(DB$data$Include), 41, 60)) {
                Vis$labelsize_nj <- 4
                Vis$tippointsize_nj <- 4
                Vis$nodepointsize_nj <- 3
                Vis$tiplab_padding_nj <- 0.15
                Vis$branch_size_nj <- 3.5
              } else if (between(sum(DB$data$Include), 61, 80)) {
                Vis$labelsize_nj <- 3.5
                Vis$tippointsize_nj <- 3.5
                Vis$nodepointsize_nj <- 2.5
                Vis$tiplab_padding_nj <- 0.1
                Vis$branch_size_nj <- 3
              } else if (between(sum(DB$data$Include), 81, 100)) {
                Vis$labelsize_nj <- 3
                Vis$tippointsize_nj <- 3
                Vis$nodepointsize_nj <- 2
                Vis$tiplab_padding_nj <- 0.1
                Vis$branch_size_nj <- 2.5
              } else {
                Vis$labelsize_nj <- 2.5
                Vis$tippointsize_nj <- 2.5
                Vis$nodepointsize_nj <- 1.5
                Vis$tiplab_padding_nj <- 0.05
                Vis$branch_size_nj <- 2
              }
            }
            
            nj_tree <- ggtree(Vis$nj)
            
            # Get upper and lower end of x range
            Vis$nj_max_x <- max(nj_tree$data$x)
            Vis$nj_min_x <- min(nj_tree$data$x)
            
            # Get parent node numbers
            Vis$nj_parentnodes <- nj_tree$data$parent
            
            # Update visualization control inputs
            nj_tiplab_size_val(Vis$labelsize_nj)
            nj_tippoint_size_val(Vis$tippointsize_nj)
            nj_nodepoint_size_val(Vis$nodepointsize_nj)
            nj_tiplab_padding_val(Vis$tiplab_padding_nj)
            nj_branch_size_val(Vis$branch_size_nj)
            nj_treescale_width_val(round(ceiling(Vis$nj_max_x) * 0.1, 0))
            nj_rootedge_length_val(round(ceiling(Vis$nj_max_x) * 0.05, 0))
            
            output$tree_plot <- renderPlot({
              make.tree()
            })
            
            Vis$nj_true <- TRUE
          }
        } else {
          
          log_print("Rendering MST graph")
          
          output$mst_field <- renderUI({
            if(isTRUE(mst_background_transparent_reactive())) {
              visNetworkOutput("tree_mst", 
                               width = paste0(mst_scale_reactive() * 
                                                as.numeric(mst_ratio_reactive()), 
                                              "px"), 
                               height = paste0(mst_scale_reactive(), "px"))
            } else {
              addSpinner(
                visNetworkOutput("tree_mst", 
                                 width = paste0(mst_scale_reactive() * 
                                                  as.numeric(mst_ratio_reactive()), 
                                                "px"), 
                                 height = paste0(mst_scale_reactive(), "px")),
                spin = "dots",
                color = "#ffffff"
              )
            }
          })
          
          if(nrow(DB$meta_true) > 100) {
            
            log_print("Over 100 isolates in MST graph")
            
            show_toast(
              title = "Computation might take a while",
              type = "warning",
              position = "bottom-end",
              timer = 10000
            )
          }
          
          meta_mst <- DB$meta_true
          Vis$meta_mst <- meta_mst
          
          # prepare igraph object
          Vis$mst_pre <- hamming_mst() |>
            as.matrix() |>
            graph.adjacency(weighted = TRUE) |>
            igraph::mst() 
          
          output$tree_mst <- renderVisNetwork({
            mst_tree()
          })
          
          Vis$mst_true <- TRUE
        }
      }
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # _______________________ ####
  
  ## Report ----
  
  observe({
    if(!is.null(DB$data)) {
      if(!is.null(input$tree_type)) {
        if(input$tree_type == "MST") {
          shinyjs::disable("rep_plot_report")
          updateCheckboxInput(session, "rep_plot_report", value = FALSE)
        } else {
          shinyjs::enable("rep_plot_report")
        }
      }
    }
  })
  
  ### Report creation UI ----
  
  observeEvent(input$create_rep, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    if((input$tree_type == "MST" & isTRUE(Vis$mst_true)) |
       (input$tree_type == "Tree" & isTRUE(Vis$nj_true))) {
      # Get currently selected missing value handling option
      if(input$na_handling == "ignore_na") {
        na_handling <- "Ignore missing values for pairwise comparison"
      } else if(input$na_handling == "omit") {
        na_handling <- "Omit loci with missing values for all assemblies"
      } else if(input$na_handling == "category") {
        na_handling <- "Treat missing values as allele variant"
      }
      
      extra_var <- character()
      if(input$tree_type == "MST") {
        shinyjs::runjs("mstReport();")
        if(isTRUE(mst_color_var_reactive())) {
          extra_var <- c(extra_var, mst_col_var_reactive())
        }
      } else if(input$tree_type == "Tree") {
        if(isTRUE(input$nj_mapping_show)) {
          extra_var <- c(extra_var, input$nj_color_mapping)
        }
        if(isTRUE(input$nj_tipcolor_mapping_show)) {
          extra_var <- c(extra_var, input$nj_tipcolor_mapping)
        }
        if(isTRUE(input$nj_tipshape_mapping_show)) {
          extra_var <- c(extra_var, input$nj_tipshape_mapping)
        }
        if(isTRUE(input$nj_tiles_show_1)) {
          extra_var <- c(extra_var, input$nj_fruit_variable)
        }
        if(isTRUE(input$nj_tiles_show_2)) {
          extra_var <- c(extra_var, input$nj_fruit_variable_2)
        }
        if(isTRUE(input$nj_tiles_show_3)) {
          extra_var <- c(extra_var, input$nj_fruit_variable_3)
        }
        if(isTRUE(input$nj_tiles_show_4)) {
          extra_var <- c(extra_var, input$nj_fruit_variable_4)
        }
        if(isTRUE(input$nj_tiles_show_5)) {
          extra_var <- c(extra_var, input$nj_fruit_variable_5)
        }
        if(isTRUE(input$nj_heatmap_show)) {
          extra_var <- c(extra_var, input$nj_heatmap_select)
        }
      }
      
      showModal(
        div(
          class = "start-modal",
          modalDialog(
            fluidRow(
              column(
                width = 12,
                fluidRow(
                  column(
                    width = 4,
                    align = "left",
                    HTML(
                      paste(
                        tags$span(style='color:white; font-size: 15px; font-weight: 900', 'General')
                      )
                    )
                  ),
                  column(
                    width = 3,
                    align = "left",
                    checkboxInput(
                      "rep_general",
                      label = "",
                      value = TRUE
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 12,
                    align = "left",
                    fluidRow(
                      column(
                        width = 3,
                        checkboxInput(
                          "rep_date_general", 
                          label = h5("Date", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 7,
                        dateInput(
                          "mst_date_general_select",
                          "",
                          max = Sys.Date()
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 3,
                        checkboxInput(
                          "rep_operator_general", 
                          label = h5("Operator", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 8,
                        textInput(
                          "mst_operator_general_select",
                          ""
                        ) 
                      )
                    ),
                    fluidRow(
                      column(
                        width = 3,
                        checkboxInput(
                          "rep_institute_general", 
                          label = h5("Institute", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 8,
                        textInput(
                          "mst_institute_general_select",
                          ""
                        ) 
                      )
                    ),
                    fluidRow(
                      column(
                        width = 3,
                        checkboxInput(
                          "rep_comm_general", 
                          label = h5("Comment", style = "color:white;")
                        )
                      ),
                      column(
                        width = 8,
                        textAreaInput(
                          inputId = "mst_comm_general_select",
                          label = "",
                          width = "100%",
                          height = "60px",
                          cols = NULL,
                          rows = NULL,
                          placeholder = NULL,
                          resize = "vertical"
                        ) 
                      )
                    )
                  )
                ),
                hr(),
                fluidRow(
                  column(
                    width = 4,
                    align = "left",
                    HTML(
                      paste(
                        tags$span(style='color: white; font-size: 15px; font-weight: 900', 'Isolate Table')
                      )
                    )
                  ),
                  column(
                    width = 3,
                    align = "left",
                    checkboxInput(
                      "rep_entrytable",
                      label = "",
                      value = TRUE
                    )
                  ),
                  column(
                    width = 4,
                    align = "left",
                    HTML(
                      paste(
                        tags$span(style='color: white; font-size: 15px; font-weight: 900', 'Include Plot')
                      )
                    )
                  ),
                  column(
                    width = 1,
                    align = "left",
                    checkboxInput(
                      "rep_plot_report",
                      label = "",
                      value = TRUE
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 6,
                    align = "left",
                    div(
                      class = "rep_tab_sel",
                      pickerInput("select_rep_tab",
                                  label = "",
                                  choices = names(DB$meta)[-2],
                                  selected = c("Assembly Name", "Scheme", "Isolation Date",
                                               "Host", "Country", "City", extra_var),
                                  options = list(
                                    size = 10,
                                    `actions-box` = TRUE,
                                    style = "background-color: white; border-radius: 5px;"
                                  ),
                                  multiple = TRUE)
                    )
                  )
                ),
                hr(),
                fluidRow(
                  column(
                    width = 4,
                    align = "left",
                    HTML(
                      paste(
                        tags$span(style='color: white; font-size: 15px; font-weight: 900', 'Analysis Parameter')
                      )
                    )
                  ),
                  column(
                    width = 3,
                    align = "left",
                    checkboxInput(
                      "rep_analysis",
                      label = "",
                      value = TRUE
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 6,
                    align = "left",
                    fluidRow(
                      column(
                        width = 4,
                        checkboxInput(
                          "rep_cgmlst_analysis",
                          label = h5("Scheme", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 8,
                        align = "right",
                        HTML(
                          paste(
                            tags$span(style='color:white; position: relative; top: 17px; font-style: italic', DB$scheme)
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(
                        width = 4,
                        checkboxInput(
                          "rep_tree_analysis",
                          label = h5("Tree", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 8,
                        align = "right",
                        HTML(
                          paste(
                            tags$span(style='color:white; position: relative; top: 17px; font-style: italic', input$tree_type)
                          )
                        )
                      )
                    )
                  ),
                  column(
                    width = 6,
                    align = "left",
                    fluidRow(
                      column(2),
                      column(
                        width = 4,
                        checkboxInput(
                          "rep_distance",
                          label = h5("Distance", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 5,
                        align = "right",
                        HTML(
                          paste(
                            tags$span(style='color:white; position: relative; top: 17px; font-style: italic', 'Hamming')
                          )
                        )
                      )
                    ),
                    fluidRow(
                      column(2),
                      column(
                        width = 4,
                        checkboxInput(
                          "rep_version",
                          label = h5("Version", style = "color:white;"),
                          value = TRUE
                        )
                      ),
                      column(
                        width = 5,
                        align = "right",
                        HTML(
                          paste(
                            tags$span(style='color:white; position: relative; top: 17px; font-style: italic', phylotraceVersion)
                          )
                        )
                      )
                    )
                  )
                ),
                fluidRow(
                  column(
                    width = 3,
                    align = "left",
                    checkboxInput(
                      "rep_missval",
                      label = h5("NA handling", style = "color:white;"),
                      value = TRUE
                    )
                  ),
                  column(
                    width = 7,
                    align = "right",
                    HTML(
                      paste(
                        tags$span(style='color:white; position: relative; top: 17px; font-style: italic; right: 35px;', na_handling)
                      )
                    )
                  )
                )
              )
            ),
            title = "cgMLST Report Generation",
            easyClose = TRUE,
            footer = tagList(
              modalButton("Cancel"),
              downloadBttn(
                "download_report",
                style = "simple",
                label = "Save",
                size = "sm",
                icon = icon("download")
              )
            )
          )
        )
      )
    } else {
      show_toast(
        title = "No tree created",
        type = "error",
        position = "bottom-end",
        timer = 6000
      )
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  observe({
    if(!is.null(input$rep_general)) {
      if(isFALSE(input$rep_general)) {
        shinyjs::disable('rep_date_general') 
        shinyjs::disable('rep_operator_general') 
        shinyjs::disable('rep_institute_general') 
        shinyjs::disable('rep_comm_general') 
        shinyjs::disable('mst_date_general_select') 
        shinyjs::disable('mst_operator_general_select') 
        shinyjs::disable('mst_institute_general_select') 
        shinyjs::disable('mst_comm_general_select') 
      } else {
        shinyjs::enable('rep_date_general') 
        shinyjs::enable('rep_operator_general') 
        shinyjs::enable('rep_institute_general') 
        shinyjs::enable('rep_comm_general')
        shinyjs::enable('mst_date_general_select') 
        shinyjs::enable('mst_operator_general_select') 
        shinyjs::enable('mst_institute_general_select') 
        shinyjs::enable('mst_comm_general_select') 
      }
    }
    
    if(!is.null(input$rep_analysis)) {
      if(isFALSE(input$rep_analysis)) {
        shinyjs::disable('rep_cgmlst_analysis') 
        shinyjs::disable('rep_tree_analysis') 
        shinyjs::disable('rep_distance') 
        shinyjs::disable('rep_missval') 
        shinyjs::disable('rep_version') 
      } else {
        shinyjs::enable('rep_cgmlst_analysis') 
        shinyjs::enable('rep_tree_analysis') 
        shinyjs::enable('rep_distance') 
        shinyjs::enable('rep_missval') 
        shinyjs::enable('rep_version') 
      }
    }
    
    if(length(input$select_rep_tab) > 0) {
      updateCheckboxInput(session, "rep_entrytable", value = TRUE)
    } else {
      updateCheckboxInput(session, "rep_entrytable", value = FALSE)
    }
  })
  
  ### Save Report ----
  
  #### Get Report elements ----
  
  observe({
    if(!is.null(DB$data)){
      if(!is.null(input$tree_type)) {
        req(c(input$rep_entrytable, input$rep_general,
              input$rep_date_general, input$rep_operator_general,
              input$rep_institute_general, input$rep_comm_general,
              input$rep_analysis, input$rep_cgmlst_analysis,
              input$rep_tree_analysis, input$rep_distance,
              input$rep_missval, input$rep_version,
              input$rep_plot_report, input$select_rep_tab))
        Report$report_df <- data.frame(Element = c("entry_table", "general_show",
                                                   "general_date", "operator",
                                                   "institute", "comment",
                                                   "analysis_show", "scheme",
                                                   "tree", "distance", "na_handling", "version",
                                                   "plot"),
                                       Include = c(input$rep_entrytable, input$rep_general,
                                                   input$rep_date_general, input$rep_operator_general,
                                                   input$rep_institute_general, input$rep_comm_general,
                                                   input$rep_analysis, input$rep_cgmlst_analysis,
                                                   input$rep_tree_analysis, input$rep_distance,
                                                   input$rep_missval, input$rep_version,
                                                   input$rep_plot_report))
      }
    }
  })
  
  #### Get Report values ----
  
  observeEvent(input$create_tree, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    if(input$tree_type == "MST") {
      Report$report_list_mst <- list(entry_table = DB$meta_true,
                                     scheme = DB$schemeinfo, 
                                     tree = input$tree_type,
                                     na_handling = if(anyNA(DB$allelic_profile_true)){input$na_handling} else {NULL},
                                     distance = "Hamming Distances",
                                     version = c(phylotraceVersion, "2.5.1"),
                                     plot = "MST")
    } else if(input$tree_type == "Tree") {
      Report$report_list_nj <- list(entry_table = DB$meta_true,
                                    scheme = DB$schemeinfo, 
                                    tree = input$tree_type,
                                    na_handling = input$na_handling,
                                    distance = "Hamming Distances",
                                    version = c(phylotraceVersion, "2.5.1"),
                                    plot = "NJ")
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Save plot for Report
  plot.report <- reactive({
    if(tree_type_reactive() == "Tree") {
      jpeg(paste0(getwd(), "/Report/NJ.jpeg"), 
           width = (as.numeric(nj_scale_val()) * 
                      as.numeric(nj_ratio_val())), 
           height = as.numeric(nj_scale_val()), quality = 100)
      print(make.tree())
      dev.off()
    } else if (tree_type_reactive() == "MST") {
      shinyjs::runjs("mstReport();")
      decoded_data <- base64enc::base64decode(input$canvas_data)
      writeBin(decoded_data, paste0(getwd(), "/Report/MST.jpg"))
    }
  })
  
  #### Event Save Report ----
  output$download_report <- downloadHandler(
    filename = function() {
      if(input$tree_type == "MST") {
        paste0("MST_Report_", Sys.Date(), ".html")
      } else if(input$tree_type == "Tree") {
        paste0("NJ_Report_", Sys.Date(), ".html")
      }
    },
    content = function(file) {
      if(input$tree_type == "MST") {
        plot.report()
        
        report <- c(Report$report_list_mst, 
                    "general_date" = as.character(input$mst_date_general_select),
                    "operator" = input$mst_operator_general_select,
                    "institute" = input$mst_institute_general_select,
                    "comment" = input$mst_comm_general_select,
                    "report_df" = Report$report_df)
        
        report[["table_columns"]] <- input$select_rep_tab
        
        # Save data to an RDS file if any elements were selected
        if (!is.null(report)) {
          
          log_print("Creating MST report")
          
          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
          
          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
          
          file.copy(paste0(getwd(), "/Report/Report.html"), file)
        } else {
          log_print("Creating MST report failed (report is null)")
        }
      } else if(input$tree_type == "Tree") {
        plot.report()
        report <- c(Report$report_list_nj, 
                    "general_date" = as.character(input$mst_date_general_select),
                    "operator" = input$mst_operator_general_select,
                    "institute" = input$mst_institute_general_select,
                    "comment" = input$mst_comm_general_select,
                    "report_df" = Report$report_df)
        
        report[["table_columns"]] <- input$select_rep_tab
        
        # Save data to an RDS file if any elements were selected
        if (!is.null(report)) {
          log_print("Creating NJ report")
          
          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
          
          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
          
          file.copy(paste0(getwd(), "/Report/Report.html"), file)
        } else {
          log_print("Creating NJ report failed (report is null)")
        }
        
      }
      
      removeModal()
    }
  )
  
  
  # _______________________ ####
  
  ## Gene Screening  ----
  
  # Check is gene screening available for species
  observe({
    req(DB$scheme)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    if(!isFALSE(amrfinder_available)) {
      Screening$available <- TRUE
    } else {
      Screening$available <- NULL
    }
  })
  
  ### Reactive Events ----
  
  # download gs plot
  output$gs_download_plot <- downloadHandler(
    filename = function() {
      fname <- paste0("GS_heatmap_", Sys.Date(), ".", input$filetype_gs)
      log_print(paste0("Save GS heatmap"))
      fname
    },
    content = function(file) {
      if (input$filetype_gs == "png") {
        png(file, width = (as.numeric(input$gs_scale) * as.numeric(input$gs_ratio)), height = as.numeric(input$gs_scale))
        print(gs_plot())
        dev.off()
      } else if (input$filetype_gs == "jpeg") {
        jpeg(file, width = (as.numeric(input$gs_scale) * as.numeric(input$gs_ratio)), height = as.numeric(input$gs_scale), quality = 100)
        print(gs_plot())
        dev.off()
      } else if (input$filetype_gs == "svg") {
        plot <- print(gs_plot())
        svg(file, 
            width = (as.numeric(input$gs_scale) * as.numeric(input$gs_ratio)) / 92,
            height = as.numeric(input$gs_scale) / 92)
        print(gs_plot())
        dev.off()
      } else if (input$filetype_gs == "bmp") {
        bmp(file, width = (as.numeric(input$gs_scale) * as.numeric(input$gs_ratio)), height = as.numeric(input$gs_scale))
        print(gs_plot())
        dev.off()
      }
    }
  )
  
  ### Screening UI Elements ----
  
  # conditional rendering of gs visualization ui
  
  output$gs_visualization_ui <- renderUI({
    req(DB$data, DB$scheme, Screening$available)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    
    if(!isFALSE(amrfinder_available)) {
      fluidRow(
        column(
          width = 2,
          align = "left",
          br(), br(), 
          div(
            class = "gs-plot-box",
            box(
              solidHeader = TRUE,
              status = "primary",
              width = "100%",
              title = "Plot Controls",
              fluidRow(
                column(
                  width = 6,
                  align = "right",
                  div(
                    id = "gs-control",
                    tipify(
                      actionBttn(
                        "gs_data_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("table-cells")
                      ),
                      title = "Data Mapping",
                      placement = "left",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "left",
                  div(
                    id = "gs-variable-menu",
                    tipify(
                      actionBttn(
                        "gs_variable_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("map-pin")
                      ),
                      title = "Variable Mapping",
                      placement = "right",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 6,
                  align = "right",
                  br(),
                  div(
                    id = "gs-control",
                    tipify(
                      actionBttn(
                        "gs_color_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("palette")
                      ),
                      title = "Colors",
                      placement = "left",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "left",
                  br(),
                  div(
                    id = "gs-size-menu",
                    tipify(
                      actionBttn(
                        "gs_size_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("up-right-and-down-left-from-center")
                      ),
                      title = "Sizing",
                      placement = "right",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                )
              ),
              fluidRow(
                column(
                  width = 6,
                  align = "right",
                  br(),
                  div(
                    id = "gs-misc-menu",
                    tipify(
                      actionBttn(
                        "gs_misc_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("ellipsis")
                      ),
                      title = "Other Settings",
                      placement = "left",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                ),
                column(
                  width = 6,
                  align = "left",
                  br(),
                  div(
                    id = "gs-download-menu",
                    tipify(
                      actionBttn(
                        "gs_download_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("download")
                      ),
                      title = "Save Plot",
                      placement = "right",
                      options = list("delay': 400, 'foo" = "foo")
                    )
                  )
                )
              )
            )
          ),
          br(),
          uiOutput("gs_plot_control_ui")
        ),
        column(
          width = 9,
          align = "left",
          br(), br(), br(), br(),
          uiOutput("gs_field")
        )
      )
    } else {NULL}
  })
  
  # gs plot control panel
  output$gs_plot_control_ui <- renderUI({
    req(Screening$available)
    if(!is.null(DB$data) & !is.null(Screening$amr_results) &
       !is.null(Screening$vir_class) & !is.null(Screening$amr_class)) {
      amr_profile_numeric <- as.data.frame(lapply(Screening$amr_results, as.numeric))
      rownames(amr_profile_numeric) <- rownames(Screening$amr_results)
      colnames(amr_profile_numeric) <- colnames(Screening$amr_results)
      heatmap_matrix <- as.matrix(amr_profile_numeric)
      
      if(!is.null(Screening$amr_class)) {
        if(nrow(Screening$amr_class) > 0) {
          amr_meta <- get.gsMeta(gene_class = Screening$amr_class, hm_matrix = heatmap_matrix)
          choices_amr <- rownames(amr_meta)[which(!is.na(amr_meta$class))]
          amr_classes <- amr_meta$class
          names(amr_classes) <- rownames(amr_meta)
          amr_classes_filtered <- na.omit(amr_classes)
          choices_amr <- list()
          for(i in 1:length(unique(amr_classes_filtered))) {
            group <- names(amr_classes_filtered)[which(amr_classes_filtered == unique(amr_classes_filtered)[i])]
            if(length(group) == 1) {
              choices_amr[[unique(amr_classes_filtered)[i]]] <- as.list(group)
            } else {
              choices_amr[[unique(amr_classes_filtered)[i]]] <- group
            }
          }
          choices_amr <- choices_amr[order(names(choices_amr))]
        } else {choices_amr <- character(0)}
      } else {choices_amr <- character(0)}
      
      if(!is.null(Screening$vir_class)) {
        if(nrow(Screening$vir_class) > 0) {
          vir_meta <- get.gsMeta(gene_class = Screening$vir_class, hm_matrix = heatmap_matrix)
          choices_vir <- rownames(vir_meta)[which(!is.na(vir_meta$class))]
          vir_classes <- vir_meta$class
          names(vir_classes) <- rownames(amr_meta)
          vir_classes_filtered <- na.omit(vir_classes)
          choices_vir <- list()
          for(i in 1:length(unique(vir_classes_filtered))) {
            group <- names(vir_classes_filtered)[which(vir_classes_filtered == unique(vir_classes_filtered)[i])]
            if(length(group) == 1) {
              choices_vir[[unique(vir_classes_filtered)[i]]] <- as.list(group)
            } else {
              choices_vir[[unique(vir_classes_filtered)[i]]] <- group
            }
          }
          choices_vir <- choices_vir[order(names(choices_vir))]
        } else {choices_vir <- character(0)}
      } else {choices_vir <- character(0)}
      
      if(all(!is.na(vir_meta$class) & !is.na(amr_meta$class))) {
        choices_noclass <- character(0)
      } else {
        choices_noclass <- rownames(amr_meta)[which(is.na(vir_meta$class) & is.na(amr_meta$class))]  
      }
      
      div(
        class = "gs-plot-box2",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Heatmap Data",
          column(
            width = 12,
            fluidRow(
              column(
                width = 12,
                align = "center",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 16px; position: relative; top: 10px;', 
                              'Isolates')
                  )
                ),
                fluidRow(
                  column(
                    width = 9,
                    div(
                      class = "gs-plot-selected-isolate",
                      pickerInput(
                        "gs_plot_selected_isolate",
                        label = "",
                        choices = list(
                          Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
                          },
                          Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
                          },
                          `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                          }
                        ),
                        choicesOpt = list(
                          disabled = c(
                            rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
                            rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
                            rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                          )
                        ),
                        selected = DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")],
                        options = list(
                          `live-search` = TRUE,
                          `actions-box` = TRUE,
                          size = 10,
                          style = "background-color: white; border-radius: 5px;"
                        ),
                        multiple = TRUE,
                        width = "96%"
                      )
                    )
                  ),
                  column(
                    width = 3,
                    align = "center",
                    dropMenu(
                      actionBttn(
                        "gsplot_isolate_label_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right-start",
                      theme = "translucent",
                      fluidRow(
                        div(
                          class = "gsplot-isolate-label",
                          selectInput(
                            "gsplot_isolate_label",
                            label = h5("Isolate Label", style = "color:white;"),
                            choices = c("Assembly ID", "Assembly Name"),
                            selected = "Assembly Name",
                            width = "70%"
                          ) 
                        )
                      )
                    ),
                    bsTooltip("gsplot_isolate_label_menu",
                              title = "Label",
                              placement = "right")
                  )
                ),
                uiOutput("gs_plot_sel_isolate_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text1",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 16px; position: relative;', 
                                'AMR Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_amr",
                    label = "",
                    choices = choices_amr,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = unlist(choices_amr),
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_amr_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 16px; position: relative;', 
                                'Virulence Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_vir",
                    label = "",
                    choices = choices_vir,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = unlist(choices_vir),
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_vir_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 15px; position: relative;', 
                                'Unclassifiable Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_noclass",
                    label = "",
                    choices = choices_noclass,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = unlist(choices_noclass),
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_noclass_info")
              )
            )
          )
        )
      )
    }
  })
  
  # gs heatmap data menu
  input_gsplot_isolate_label <- reactive({input$gsplot_isolate_label}) %>% debounce(1000)
  
  observeEvent(input$gs_data_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    if(!is.null(input_gsplot_isolate_label())) {
      gsplot_isolate_label_selected <- input_gsplot_isolate_label()
    } else {
      gsplot_isolate_label_selected <- "Assembly Name"
    }
    
    if(!is.null(gs_plot_selected_isolate())) {
      gs_plot_selected_isolate_selected <- gs_plot_selected_isolate()
    } else {
      gs_plot_selected_isolate_selected <- DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
    }
    
    amr_profile_numeric <- as.data.frame(lapply(Screening$amr_results, as.numeric))
    rownames(amr_profile_numeric) <- rownames(Screening$amr_results)
    colnames(amr_profile_numeric) <- colnames(Screening$amr_results)
    heatmap_matrix <- as.matrix(amr_profile_numeric)
    
    if(!is.null(Screening$amr_class)) {
      if(nrow(Screening$amr_class) > 0) {
        amr_meta <- get.gsMeta(gene_class = Screening$amr_class, hm_matrix = heatmap_matrix)
        choices_amr <- rownames(amr_meta)[which(!is.na(amr_meta$class))]
        amr_classes <- amr_meta$class
        names(amr_classes) <- rownames(amr_meta)
        amr_classes_filtered <- na.omit(amr_classes)
        choices_amr <- list()
        for(i in 1:length(unique(amr_classes_filtered))) {
          group <- names(amr_classes_filtered)[which(amr_classes_filtered == unique(amr_classes_filtered)[i])]
          if(length(group) == 1) {
            choices_amr[[unique(amr_classes_filtered)[i]]] <- as.list(group)
          } else {
            choices_amr[[unique(amr_classes_filtered)[i]]] <- group
          }
        }
      } else {choices_amr <- character(0)}
    } else {choices_amr <- character(0)}
    
    gs_plot_selected_amr_selected <- gs_plot_selected_amr()
    
    if(!is.null(Screening$vir_class)) {
      if(nrow(Screening$vir_class) > 0) {
        vir_meta <- get.gsMeta(gene_class = Screening$vir_class, hm_matrix = heatmap_matrix)
        choices_vir <- rownames(vir_meta)[which(!is.na(vir_meta$class))]
        vir_classes <- vir_meta$class
        names(vir_classes) <- rownames(amr_meta)
        vir_classes_filtered <- na.omit(vir_classes)
        choices_vir <- list()
        for(i in 1:length(unique(vir_classes_filtered))) {
          group <- names(vir_classes_filtered)[which(vir_classes_filtered == unique(vir_classes_filtered)[i])]
          if(length(group) == 1) {
            choices_vir[[unique(vir_classes_filtered)[i]]] <- as.list(group)
          } else {
            choices_vir[[unique(vir_classes_filtered)[i]]] <- group
          }
        }
      } else {choices_vir <- character(0)}
    } else {choices_vir <- character(0)}
    
    gs_plot_selected_vir_selected <- gs_plot_selected_vir()
    
    if(all(!is.na(vir_meta$class) & !is.na(amr_meta$class))) {
      choices_noclass <- character(0)
    } else {
      choices_noclass <- rownames(amr_meta)[which(is.na(vir_meta$class) & is.na(amr_meta$class))]  
    }
    
    gs_plot_selected_noclass_selected <- gs_plot_selected_noclass()
    
    output$gs_plot_control_ui <- renderUI(
      div(
        class = "gs-plot-box2",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Heatmap Data",
          column(
            width = 12,
            fluidRow(
              column(
                width = 12,
                align = "center",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 16px; position: relative; top: 10px;', 
                              'Isolates')
                  )
                ),
                fluidRow(
                  column(
                    width = 9,
                    div(
                      class = "gs-plot-selected-isolate",
                      pickerInput(
                        "gs_plot_selected_isolate",
                        label = "",
                        choices = list(
                          Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
                          },
                          Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
                          },
                          `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
                            as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
                          } else {
                            DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                          }
                        ),
                        choicesOpt = list(
                          disabled = c(
                            rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
                            rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
                            rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                          )
                        ),
                        selected = gs_plot_selected_isolate_selected,
                        options = list(
                          `live-search` = TRUE,
                          `actions-box` = TRUE,
                          size = 10,
                          style = "background-color: white; border-radius: 5px;"
                        ),
                        multiple = TRUE,
                        width = "96%"
                      )
                    )
                  ),
                  column(
                    width = 3,
                    align = "center",
                    dropMenu(
                      actionBttn(
                        "gsplot_isolate_label_menu",
                        label = "",
                        color = "default",
                        size = "sm",
                        style = "material-flat",
                        icon = icon("sliders")
                      ),
                      placement = "right-start",
                      theme = "translucent",
                      fluidRow(
                        div(
                          class = "gsplot-isolate-label",
                          selectInput(
                            "gsplot_isolate_label",
                            label = h5("Isolate Label", style = "color:white;"),
                            choices = c("Assembly ID", "Assembly Name"),
                            selected = gsplot_isolate_label_selected,
                            width = "70%"
                          ) 
                        )
                      )
                    )
                  )
                ),
                uiOutput("gs_plot_sel_isolate_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text1",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 16px; position: relative;', 
                                'AMR Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_amr",
                    label = "",
                    choices = choices_amr,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = gs_plot_selected_amr_selected,
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_amr_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 16px; position: relative;', 
                                'Virulence Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_vir",
                    label = "",
                    choices = choices_vir,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = gs_plot_selected_vir_selected,
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_vir_info")
              ),
              column(
                width = 12,
                align = "center",
                br(),
                div(
                  class = "gs-heatmap-text",
                  HTML(
                    paste(
                      tags$span(style='color: white; font-size: 15px; position: relative;', 
                                'Unclassifiable Genes')
                    )
                  )
                ),
                div(
                  class = "gs-plot-selected-isolate",
                  pickerInput(
                    "gs_plot_selected_noclass",
                    label = "",
                    choices = choices_noclass,
                    options = list(
                      `live-search` = TRUE,
                      `actions-box` = TRUE,
                      size = 10,
                      style = "background-color: white; border-radius: 5px;"
                    ),
                    selected = gs_plot_selected_noclass_selected,
                    multiple = TRUE,
                    width = "96%"
                  )
                ),
                uiOutput("gs_plot_sel_noclass_info")
              )
            )
          )
        )
      )
    )
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # color menu
  observeEvent(input$gs_color_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    if(!is.null(gsplot_color_text())) {
      gsplot_color_text_selected <- gsplot_color_text()
    } else {
      gsplot_color_text_selected <- "#000000"
    }
    
    if(!is.null(gsplot_color_dend())) {
      gsplot_color_dend_selected <- gsplot_color_dend()
    } else {
      gsplot_color_dend_selected <- "#000000"
    }
    
    if(!is.null(gsplot_color_palette1())) {
      gsplot_color_palette1_selected <- gsplot_color_palette1()
    } else {
      gsplot_color_palette1_selected <- "#66C2A5"
    }
    
    if(!is.null(gsplot_color_palette2())) {
      gsplot_color_palette2_selected <- gsplot_color_palette2()
    } else {
      gsplot_color_palette2_selected <- "#E5C494"
    }
    
    if(!is.null(gsplot_grid_color())) {
      gsplot_grid_color_selected <- gsplot_grid_color()
    } else {
      gsplot_grid_color_selected <- "#ffffff"
    }
    
    if(!is.null(gsplot_background())) {
      gsplot_background_selected <- gsplot_background()
    } else {
      gsplot_background_selected <- "#ffffff"
    }
    
    output$gs_plot_control_ui <- renderUI({
      
      req(Screening$available)
      
      div(
        class = "gs-plot-box3",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Color Menu",
          column(
            width = 12,
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Text')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_color_text",
                  selected = gsplot_color_text_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Dendrogram')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_color_dend",
                  selected = gsplot_color_dend_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Present')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_color_palette1",
                  selected = gsplot_color_palette1_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Absent')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_color_palette2",
                  selected = gsplot_color_palette2_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Grid Color')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_grid_color",
                  selected = gsplot_grid_color_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 10px;', 
                              'Background')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                colorPickr(
                  inputId = "gsplot_background",
                  selected = gsplot_background_selected,
                  label = "",
                  update = "changestop",
                  interaction = list(clear = FALSE,
                                     save = FALSE),
                  position = "right-start",
                  width = "120px"
                ),
                br()
              )
            )
          )
        )
      )
    })  
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # variable mapping menu
  input_gs_amr_variables <- reactive({input$gs_amr_variables}) %>% debounce(1000)
  input_gs_vir_variables <- reactive({input$gs_vir_variables}) %>% debounce(1000)
   
  observeEvent(input$gs_variable_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    output$gs_plot_control_ui <- renderUI({
      
      req(Screening$available)
      
      if(!is.null(input_gs_amr_variables())) {
        gs_amr_variables_selected <- input_gs_amr_variables()
      } else {
        gs_amr_variables_selected <- "Classification"
      }
      
      if(!is.null(input_gs_vir_variables())) {
        gs_vir_variables_selected <- input_gs_vir_variables()
      } else {
        gs_vir_variables_selected <- "Classification"
      }
      
      shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                            "#gs_virclass_scale",
                                            color_scale_bg_JS)))
      
      shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                            "#gs_amrclass_scale",
                                            color_scale_bg_JS)))
      
      shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                            "#gs_mapping_scale",
                                            color_scale_bg_JS)))
      
      div(
        class = "gs-plot-box2",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Variable Mapping",
          column(
            width = 12,
            fluidRow(
              column(
                width = 12,
                align = "center",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 16px; position: relative; top: 10px',
                              'Isolate Variables')
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 37px;', 
                              'Variable')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                uiOutput("gs_var_mapping_ui"),
                br()
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 9px;', 
                              'Scale')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                uiOutput("gs_mapping_scale_ui"),
                br()
              )
            ),
            fluidRow(
              column(
                width = 12,
                align = "center",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 16px; position: relative;',
                              'AMR Genes')
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 27px;', 
                              'Variable')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                div(
                  class = "gs-var-mapping-sel",
                  selectInput(
                    "gs_amr_variables",
                    "",
                    choices = c("Classification", "None"),
                    selected = gs_amr_variables_selected,
                    width = "100%"
                  )
                ),
                br()
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 9px;', 
                              'Scale')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                uiOutput("gs_amrclass_scale_ui")
              )
            ),
            fluidRow(
              column(
                width = 12,
                align = "center",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 16px; position: relative;',
                              'Virulence Genes')
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 27px;', 
                              'Variable')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                div(
                  class = "gs-var-mapping-sel",
                  selectInput(
                    "gs_vir_variables",
                    "",
                    choices = c("Classification", "None"),
                    selected = gs_vir_variables_selected,
                    width = "100%"
                  )
                ),
                br()
              )
            ),
            fluidRow(
              column(
                width = 4,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px; top: 9px;', 
                              'Scale')
                  )
                )
              ),
              column(
                width = 8,
                align = "center",
                uiOutput("gs_virclass_scale_ui")
              )
            )
          )
        )
      )
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # sizing menu
  input_gsplot_grid_width <- reactive({input$gsplot_grid_width}) %>% debounce(1000)
  input_gsplot_legend_labelsize <- reactive({input$gsplot_legend_labelsize}) %>% debounce(1000)
  input_gsplot_fontsize_title <- reactive({input$gsplot_fontsize_title}) %>% debounce(1000)
  input_gsplot_treeheight_col <- reactive({input$gsplot_treeheight_col}) %>% debounce(1000)
  input_gsplot_treeheight_row <- reactive({input$gsplot_treeheight_row}) %>% debounce(1000)
  
  observeEvent(input$gs_size_menu, {
    
    req(Screening$available)
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    output$gs_plot_control_ui <- renderUI({
      
      if(!is.null(input_gsplot_grid_width())) {
        gsplot_grid_width_selected <- input_gsplot_grid_width()
      } else {
        gsplot_grid_width_selected <- 1
      }
      
      if(!is.null(input_gsplot_legend_labelsize())) {
        gsplot_legend_labelsize_selected <- input_gsplot_legend_labelsize()
      } else {
        gsplot_legend_labelsize_selected <- 9
      }
      
      if(!is.null(input_gsplot_fontsize_title())) {
        gsplot_fontsize_title_selected <- input_gsplot_fontsize_title()
      } else {
        gsplot_fontsize_title_selected <- 16
      }
      
      if(!is.null(input_gsplot_treeheight_col())) {
        gsplot_treeheight_col_selected <- input_gsplot_treeheight_col()
      } else {
        gsplot_treeheight_col_selected <- 2
      }
      
      if(!is.null(input_gsplot_treeheight_row())) {
        gsplot_treeheight_row_selected <- input_gsplot_treeheight_row()
      } else {
        gsplot_treeheight_row_selected <- 2
      }
      
      div(
        class = "gs-plot-box3",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Sizing Menu",
          column(
            width = 12,
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 12px;',
                              'Legend')
                  )
                )
              ),
              column(
                width = 6,
                div(
                  class = "gs-slider",
                  sliderInput(
                    "gsplot_legend_labelsize",
                    "",
                    value = gsplot_legend_labelsize_selected,
                    max = 14,
                    min = 6,
                    ticks = FALSE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 12px;',
                              'Grid Width')
                  )
                )
              ),
              column(
                width = 6,
                div(
                  class = "gs-slider",
                  sliderInput(
                    "gsplot_grid_width",
                    "",
                    value = gsplot_grid_width_selected,
                    max = 3,
                    min = 0,
                    ticks = FALSE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 12px; position: relative; top: 12px;',
                              'Row/Col Titles')
                  )
                )
              ),
              column(
                width = 6,
                div(
                  class = "gs-slider",
                  sliderInput(
                    "gsplot_fontsize_title",
                    "",
                    value = gsplot_fontsize_title_selected,
                    max = 24,
                    min = 8,
                    ticks = FALSE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 12px;',
                              'Dendro Cols')
                  )
                )
              ),
              column(
                width = 6,
                div(
                  class = "gs-slider",
                  sliderInput(
                    "gsplot_treeheight_col",
                    "",
                    value = gsplot_treeheight_col_selected,
                    max = 10,
                    min = 1,
                    ticks = FALSE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 13px; position: relative; top: 12px;',
                              'Dendro Rows')
                  )
                )
              ),
              column(
                width = 6,
                div(
                  class = "gs-slider",
                  sliderInput(
                    "gsplot_treeheight_row",
                    "",
                    value = gsplot_treeheight_row_selected,
                    max = 10,
                    min = 1,
                    ticks = FALSE
                  )
                ),
                br()
              )
            )
          )
        )
      )
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # download menu
  observeEvent(input$gs_download_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    output$gs_plot_control_ui <- renderUI({
      req(Screening$available)
      
      div(
        class = "gs-plot-box4",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Save Heatmap",
          column(
            width = 12,
            align = "center",
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; left: 10px;',
                              'Save As')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                div(
                  class = "filetype-gs",
                  selectInput(
                    inputId = "filetype_gs",
                    label = "",
                    choices = c("png", "jpeg", "bmp", "svg")
                  )
                ),
                br(), br()
              )
            ),
            downloadBttn(
              "gs_download_plot",
              style = "simple",
              label = "",
              size = "sm",
              icon =  icon("download"),
              color = "primary"
            ),
            br(), br()
          )
        )
      )
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
 
  input_gs_ratio <- reactive({input$gs_ratio}) %>% debounce(1000)
  input_gs_scale<- reactive({input$gs_scale}) %>% debounce(1000)
  input_gs_cluster_row <- reactive({input$gs_cluster_row}) %>% debounce(1000)
  input_gs_cluster_col<- reactive({input$gs_cluster_col}) %>% debounce(1000)
  input_gs_cluster_distance_col <- reactive({input$gs_cluster_distance_col}) %>% debounce(1000)
  input_gs_cluster_distance_row <- reactive({input$gs_cluster_distance_row}) %>% debounce(1000)
  input_gs_cluster_method_col <- reactive({input$gs_cluster_method_col}) %>% debounce(1000)
  input_gs_cluster_method_row <- reactive({input$gs_cluster_method_row}) %>% debounce(1000)
  
  # miscellaneous menu
  observeEvent(input$gs_misc_menu, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    output$gs_plot_control_ui <- renderUI({
      req(Screening$available)
      
      if(!is.null(input_gs_ratio())) {
        gs_ratio_selected <- input_gs_ratio()
        if(input_gs_ratio() == "1.6") {
          min <- 500
          max <- 1200
          step <- 5
        } else if(input_gs_ratio() == "1.77777777777778") {
          min <- 504
          max <- 1197
          step <- 9
        } else if(input_gs_ratio() == "1.33333333333333") {
          min <- 501
          max <- 1200
          step <- 3
        }
      } else {
        gs_ratio_selected <- c("16:9" = (16/9))
        min <- 504
        max <- 1197
        step <- 9
      }
      
      if(!is.null(input_gs_scale())) {
        gs_scale_selected <- input_gs_scale()
      } else {
        gs_scale_selected <- 702
      }
      
      if(!is.null(input_gs_cluster_col())) {
        gs_cluster_col_selected <- input_gs_cluster_col()
      } else {
        gs_cluster_col_selected <- TRUE
      }
      
      if(!is.null(input_gs_cluster_row())) {
        gs_cluster_row_selected <- input_gs_cluster_row()
      } else {
        gs_cluster_row_selected <- TRUE
      }
      
      if(!is.null(input_gs_cluster_distance_col())) {
        gs_cluster_distance_col_selected <- input_gs_cluster_distance_col()
      } else {
        gs_cluster_distance_col_selected <- "binary"
      }
      
      if(!is.null(input_gs_cluster_distance_row())) {
        gs_cluster_distance_row_selected <- input_gs_cluster_distance_row()
      } else {
        gs_cluster_distance_row_selected <- "binary"
      }
      
      if(!is.null(input_gs_cluster_method_col())) {
        gs_cluster_method_col_selected <- input_gs_cluster_method_col()
      } else {
        gs_cluster_method_col_selected <- "average"
      }
      
      if(!is.null(input_gs_cluster_method_row())) {
        gs_cluster_method_row_selected <- input_gs_cluster_method_row()
      } else {
        gs_cluster_method_row_selected <- "average"
      }
      
      div(
        class = "gs-plot-box2",
        box(
          solidHeader = TRUE,
          status = "primary",
          width = "100%",
          title = "Miscellaneous",
          column(
            width = 12,
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative;',
                              'Ratio')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                div(
                  class = "gs-ratio",
                  selectInput(
                    "gs_ratio",
                    "",
                    choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3)),
                    selected = gs_ratio_selected
                  )
                )
              )
            ),
            br(),
            fluidRow(
              column(
                width = 6,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 14px; position: relative; top: 7px;',
                              'Scale')
                  )
                )
              ),
              div(
                class = "gs-slider-col",
                column(
                  width = 6,
                  align = "center",
                  div(
                    class = "gs-slider-scale",
                    sliderInput(
                      "gs_scale",
                      "",
                      min = min,
                      max = max,
                      value = gs_scale_selected,
                      step = step,
                      width = "95%",
                      ticks = FALSE
                    )
                  )
                )
              )
            ),
            hr(),
            fluidRow(
              column(
                width = 8,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; position: relative; top: 5px;',
                              'Cluster Columns')
                  )
                )
              ),
              column(
                width = 4,
                align = "left",
                div(
                  class = "mat-switch-gs-settings",
                  materialSwitch(
                    "gs_cluster_col",
                    "",
                    value = gs_cluster_col_selected,
                    right = TRUE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                br(),
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 12px; position: relative; top: -12px;',
                              'Distance Algorithm')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                br(),
                div(
                  class = "gs-cluster-sel",
                  selectInput(
                    "gs_cluster_distance_col",
                    "",
                    choices = c("Binary" = "binary", "Hamming" = "hamming", "MCC" = "mcc"),
                    selected = gs_cluster_distance_col_selected
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                br(),
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 12px; position: relative; top: -12px;',
                              'Agglom. Method')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                br(),
                div(
                  class = "gs-cluster-sel",
                  selectInput(
                    "gs_cluster_method_col",
                    "",
                    choices = c("ward.D" = "ward.D", "ward.D2"= "ward.D2", 
                                "Single" = "single", "Complete" = "complete", 
                                "UPGMA" = "average", "WPGMA"  = "mcquitty", 
                                "WPGMC" = "median", "UPGMC" = "centroid"),
                    selected = gs_cluster_method_col_selected
                  )
                )
              )
            ),
            hr(),
            fluidRow(
              column(
                width = 8,
                align = "left",
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 15px; position: relative; top: 4px;',
                              'Cluster Rows')
                  )
                )
              ),
              column(
                width = 4,
                align = "left",
                div(
                  class = "mat-switch-gs-settings",
                  materialSwitch(
                    "gs_cluster_row",
                    "",
                    value = gs_cluster_row_selected,
                    right = TRUE
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                br(),
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 12px; position: relative; top: -12px;',
                              'Distance Algorithm')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                br(),
                div(
                  class = "gs-cluster-sel",
                  selectInput(
                    "gs_cluster_distance_row",
                    "",
                    choices = c("Binary" = "binary", "Hamming" = "hamming", "MCC" = "mcc"),
                    selected = gs_cluster_distance_row_selected
                  )
                )
              )
            ),
            fluidRow(
              column(
                width = 6,
                align = "left",
                br(),
                HTML(
                  paste(
                    tags$span(style='color: white; font-size: 12px; position: relative; top: -12px;',
                              'Agglom. Method')
                  )
                )
              ),
              column(
                width = 6,
                align = "center",
                br(),
                div(
                  class = "gs-cluster-sel",
                  selectInput(
                    "gs_cluster_method_row",
                    "",
                    selectize = TRUE,
                    choices = c("ward.D" = "ward.D", "ward.D2"= "ward.D2", 
                                "Single" = "single", "Complete" = "complete", 
                                "UPGMA" = "average", "WPGMA"  = "mcquitty", 
                                "WPGMC" = "median", "UPGMC" = "centroid"),
                    selected = gs_cluster_method_row_selected
                  )
                )
              )
            )
          )
        )
      )
    })
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  }) 
  
  # gs classification scale 
  output$gs_virclass_scale_ui <- renderUI({
    req(Screening$available)
    
    if(!is.null(Screening$hm_meta)) {
      if(length(unique(Screening$hm_meta$vir)) > 7) {
        
        if(!is.null(gs_virclass_scale())) {
          gs_virclass_scale_selected <- gs_virclass_scale()
        } else {
          gs_virclass_scale_selected <- "#turbo"
        }
        
        gs_virclass_scale <- selectInput(
          "gs_virclass_scale",
          "",
          choices = list(
            Gradient = gradient_scales
          ),
          selected = gs_virclass_scale_selected,
          width = "100%"
        )
        
      } else {
        
        if(!is.null(gs_virclass_scale())) {
          gs_virclass_scale_selected <- gs_virclass_scale()
        } else {
          gs_virclass_scale_selected <- "Set1"
        }
        
        gs_virclass_scale <- selectInput(
          "gs_virclass_scale",
          "",
          choices = list(
            Qualitative = qualitative_scales,
            Gradient = gradient_scales
          ),
          selected = gs_virclass_scale_selected,
          width = "100%"
        )
      }
      
    } else {
      
      if(!is.null(gs_virclass_scale())) {
        gs_virclass_scale_selected <- gs_virclass_scale()
      } else {
        gs_virclass_scale_selected <- "turbo"
      }
        
      gs_virclass_scale <- selectInput(
        "gs_virclass_scale",
        "",
        choices = list(
          Gradient = gradient_scales
        ),
        selected = gs_virclass_scale_selected,
        width = "100%"
      )
      
    }
    
    shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                          "#gs_virclass_scale",
                                          color_scale_bg_JS)))
    
    div(
      class = "gs-vir-class-scale",
      gs_virclass_scale
    )
  })
  
  output$gs_amrclass_scale_ui <- renderUI({
    req(Screening$available)
    
    if(!is.null(Screening$hm_meta)) {
      if(length(unique(Screening$hm_meta$amr)) > 7) {
        
        if(!is.null(gs_amrclass_scale())) {
          gs_amrclass_scale_selected <- gs_amrclass_scale()
        } else {
          gs_amrclass_scale_selected <- "turbo"
        }
        
        gs_amrclass_scale <- selectInput(
          "gs_amrclass_scale",
          "",
          choices = list(
            Gradient = gradient_scales
          ),
          selected = gs_amrclass_scale_selected,
          width = "100%"
        )
        
      } else {
        
        if(!is.null(gs_amrclass_scale())) {
          gs_amrclass_scale_selected <- gs_amrclass_scale()
        } else {
          gs_amrclass_scale_selected <- "Set1"
        }
        
        gs_amrclass_scale <- selectInput(
          "gs_amrclass_scale",
          "",
          choices = list(
            Qualitative = qualitative_scales,
            Gradient = gradient_scales
          ),
          selected = gs_amrclass_scale_selected,
          width = "100%"
        )
      }
      
    } else {
      
      if(!is.null(gs_amrclass_scale())) {
        gs_amrclass_scale_selected <- gs_amrclass_scale()
      } else {
        gs_amrclass_scale_selected <- "turbo"
      }
      
      gs_amrclass_scale <- selectInput(
        "gs_amrclass_scale",
        "",
        choices = list(
          Gradient = gradient_scales,
        ),
        selected = gs_amrclass_scale_selected,
        width = "100%"
      )
    }
    
    shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                          "#gs_amrclass_scale",
                                          color_scale_bg_JS)))
    
    div(
      class = "gs-amr-class-scale",
      gs_amrclass_scale
    )
  })
  
  # gs variable mapping scale 
  output$gs_mapping_scale_ui <- renderUI({
    req(input$gs_var_mapping, Screening$available)
    
    if(input$gs_var_mapping != "None") {
      if(class(unlist(DB$meta[,input$gs_var_mapping])) == "numeric") {
        
        if(!is.null(gs_mapping_scale())) {
          gs_mapping_scale_selected <- gs_mapping_scale()
        } else {
          gs_mapping_scale_selected <- "magma"
        }
        
        gs_mapping_scale <- selectInput(
          "gs_mapping_scale",
          "",
          choices = list(
            Continous = gradient_scales,
            Diverging = diverging_scales
          ),
          width = "100%",
          selected = gs_mapping_scale_selected
        )
        
      } else {
        if(length(unique(unlist(DB$meta[input$gs_var_mapping]))) > 7) {
          
          if(!is.null(gs_mapping_scale())) {
            gs_mapping_scale_selected <- gs_mapping_scale()
          } else {
            gs_mapping_scale_selected <- "magma"
          }
          
          gs_mapping_scale <- selectInput(
            "gs_mapping_scale",
            "",
            choices = list(
              Gradient = gradient_scales
            ),
            selected = gs_mapping_scale_selected,
            width = "100%"
          )
          
        } else {
          
          if(!is.null(gs_mapping_scale())) {
            gs_mapping_scale_selected <- gs_mapping_scale()
          } else {
            gs_mapping_scale_selected <- "Set1"
          }
          
          gs_mapping_scale <- selectInput(
            "gs_mapping_scale",
            "",
            choices = list(
              Qualitative = qualitative_scales,
              Sequential = sequential_scales
            ),
            selected = gs_mapping_scale_selected,
            width = "100%"
          )
          
        }
      }
    } else {
      
      if(!is.null(gs_mapping_scale())) {
        gs_mapping_scale_selected <- gs_mapping_scale()
      } else {
        gs_mapping_scale_selected <- "Set1"
      }
      
      gs_mapping_scale <- selectInput(
        "gs_mapping_scale",
        "",
        choices = list(
          Qualitative = qualitative_scales,
          Sequential = sequential_scales
        ),
        selected = gs_mapping_scale_selected,
        width = "100%"
      )
      
    }
    
    shinyjs::delay(0, shinyjs::runjs(gsub("#col_scale_id",
                                          "#gs_mapping_scale",
                                          color_scale_bg_JS)))
      
    div(
      class = "gs-mapping-scale",
      gs_mapping_scale
    )
  })
  
  # variable mapping
  input_gs_var_mapping <- reactive({input$gs_var_mapping}) %>% debounce(1000)
  
  output$gs_var_mapping_ui <- renderUI({
    req(DB$meta, Screening$available)
    
    if(!is.null(input_gs_var_mapping())) {
      gs_var_mapping_selected <- input_gs_var_mapping()
    } else {
      gs_var_mapping_selected <- "None"
    }
    
    div(
      class = "gs-var-mapping-sel",
      selectInput(
        "gs_var_mapping",
        "",
        choices = if(ncol(DB$meta) == 13) {
          c(
            None = "None",
            `Isolation Date` = "Isolation Date",
            Host = "Host",
            Country = "Country",
            City = "City"
          )
        } else {
          append(c(None = "None", `Isolation Date` = "Isolation Date", Host = "Host", 
                   Country = "Country", City = "City"),
                 colnames(DB$meta)[14:ncol(DB$meta)])
        },
        width = "100%",
        selected = gs_var_mapping_selected
      )
    )
  })
  
  output$gs_field <- renderUI({
    req(Screening$available)
    
    if(!is.null(input$gs_scale)) {
      gs_scale <- input$gs_scale
    } else {
      gs_scale <- 702
    }
    if(!is.null(input$gs_ratio)) {
      gs_ratio <- input$gs_ratio
    } else {
      gs_ratio <- c("16:9" = (16/9))
    }
    
    addSpinner(
      plotOutput("gs_plot", width = paste0(as.character(as.numeric(gs_scale) * as.numeric(gs_ratio)), "px"), height = paste0(as.character(gs_scale), "px")),
      spin = "dots",
      color = "#ffffff"
    )
  })
  
  # Render isolate picker info text
  output$gs_plot_sel_isolate_info <- renderUI({
    req(DB$data, Screening$available)
    
    if(is.null(input$gs_plot_selected_isolate)) {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative;  ', 
                  "0 isolates(s) selected"),
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative;  ', 
                  "Select min. 3 isolates")
      )
    } else if(length(input$gs_plot_selected_isolate) < 3) {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative;  ', 
                  paste(
                    length(input$gs_plot_selected_isolate),
                    'isolate(s) selected'
                  )),
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative;  ', 
                  "Select min. 3 isolates")
      )
    } else {
      tagList(
        tags$span(style='color: white; font-size: 12px; font-style: italic; position: relative;  ', 
                  paste(
                    length(input$gs_plot_selected_isolate),
                    'isolate(s) selected'
                  )),
        tags$br(),
        tags$span(style='color: #282F38; font-style: italic; font-size: 12px; position: relative;  ', 
                  "Select min. 3 isolates")
      )
    }
  })
  
  # Render gene picker info texts
  output$gs_plot_sel_amr_info <- renderUI({
    req(DB$data, Screening$available)
    
    if(is.null(input$gs_plot_selected_amr)) {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative;', 
                  "0 gene(s) selected"),
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative;', 
                  "Select min. 3 genes")
      )
    } else if(length(input$gs_plot_selected_amr) < 3) {
      tagList(
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative;',
                  paste(length(input$gs_plot_selected_amr),
                        "gene(s) selected")), 
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative;', 
                  "Select min. 3 genes")
      )
    } else {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative;', 
                  paste(length(input$gs_plot_selected_amr),
                        "gene(s) selected")),
        tags$br(),
        tags$span(style='color: #282F38; font-style: italic; font-size: 12px; position: relative;', 
                  "Select min. 3 genes")
      )
    }
  })
  
  output$gs_plot_sel_vir_info <- renderUI({
    req(DB$data, Screening$available)
    
    if(is.null(input$gs_plot_selected_vir)) {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative; ', 
                  "0 gene(s) selected"),
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    } else if(length(input$gs_plot_selected_vir) < 3) {
      tagList(
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ',
                  paste(length(input$gs_plot_selected_vir),
                        "gene(s) selected")), 
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    } else {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative; ', 
                  paste(length(input$gs_plot_selected_vir),
                        "gene(s) selected")),
        tags$br(),
        tags$span(style='color: #282F38; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    }
  })
  
  output$gs_plot_sel_noclass_info <- renderUI({
    req(DB$data, Screening$available)
    
    if(is.null(input$gs_plot_selected_noclass)) {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative; ', 
                  "0 gene(s) selected"),
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    } else if(length(input$gs_plot_selected_noclass) < 3) {
      tagList(
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ',
                  paste(length(input$gs_plot_selected_noclass),
                        "gene(s) selected")), 
        tags$br(),
        tags$span(style='color: orange; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    } else {
      tagList(
        tags$span(style='color: white; font-style: italic; font-size: 12px; position: relative; ', 
                  paste(length(input$gs_plot_selected_noclass),
                        "gene(s) selected")),
        tags$br(),
        tags$span(style='color: #282F38; font-style: italic; font-size: 12px; position: relative; ', 
                  "Select min. 3 genes")
      )
    }
  })
  
  # Rendering results table
  output$gs_results_table <- renderUI({
    req(DB$data, Screening$available)
    if(!is.null(input$gs_profile_select)) {
      if(length(input$gs_profile_select) > 0 & any(input$gs_profile_select %in% DB$data$`Assembly ID`)) {
        fluidRow(
          div(class = "loci_table",
              DT::dataTableOutput("gs_profile_table")),
          br(),
          HTML(
            paste0("<span style='color: white; font-size: 12px'>", 
                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
            
          )
        )
      } else {
        fluidRow(
          br(), br(),
          p(
            HTML(
              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
                     'Select entry from the table to display resistance profile')
              
            )
          )
        )
      }
    } else {
      fluidRow(
        br(), br(),
        p(
          HTML(
            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
                   'Select entry from the table to display resistance profile')
            
          )
        )
      )
    }
  })
  
  # Gene screening download button
  output$gs_download <- renderUI({
    req(DB$data, Screening$available)
    
    if(!is.null(input$gs_profile_select)) {
      if(length(input$gs_profile_select) > 0) {
        fluidRow(
          downloadBttn(
            "download_resistance_profile",
            style = "simple",
            label = "Profile Table",
            size = "sm",
            icon = icon("download"),
            color = "primary"
          ),
          bsTooltip("download_resistance_profile_bttn", 
                    HTML(paste0("Save resistance profile table for</br>",
                                input$gs_profile_select)), 
                    placement = "bottom", trigger = "hover")
        )
      } else {NULL}
    } else {NULL}
  })
  
  # Resistance profile table output display
  output$gs_profile_display <- renderUI({
    req(DB$data, Screening$available)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    if(!isFALSE(amrfinder_available)) {
      if(!is.null(DB$meta_gs)) {
        column(
          width = 10,
          fluidRow(
            column(
              width = 4,
              p(
                HTML(
                  paste0("<span style='color: white; font-size: 18px'>", 
                         "Gene Screening Results</br>",
                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
                         "Comprising genes for resistance, virulence, stress, etc.")
                )
              )
            ),
            column(
              width = 3,
              div(
                class = "gs-picker",
                pickerInput(
                  "gs_profile_select",
                  "",
                  choices = list(
                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
                    } else {
                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
                    },
                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
                    } else {
                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
                    },
                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
                    } else {
                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                    }
                  ),
                  choicesOpt = list(
                    disabled = c(
                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                    )
                  ),
                  options = list(
                    `live-search` = TRUE,
                    size = 10,
                    style = "background-color: white; border-radius: 5px;"
                  )
                )
              )
            ),
            column(
              width = 1,
              actionButton(
                "gs_table_view",
                "",
                icon = icon("table-list")
              ),
              bsTooltip("gs_table_view", 
                        HTML("Select from table"), 
                        placement = "bottom", trigger = "hover")
            ),
            column(
              width = 3,
              align = "center",
              uiOutput("gs_download")
            )
          ),
          br(),
          uiOutput("gs_results_table")
        )
      } else {NULL}
    } else {NULL}
  })
  
  # Resistance profile table
  observe({
    req(Screening$available, DB$meta_gs, input$gs_profile_select, Startup$database, DB$scheme, DB$data)
    
    if(length(input$gs_profile_select) > 0 & any(input$gs_profile_select %in% DB$data$`Assembly ID`)) {
      iso_select <- input$gs_profile_select
      iso_path <- file.path(Startup$database, gsub(" ", "_", DB$scheme), "Isolates", 
                            iso_select, "amrfinder.out")
      
      if(file.exists(iso_path)) {
        res_profile <- read.delim(iso_path)
        
        colnames(res_profile) <- c(
          "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
          "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
          "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
          "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
        
        Screening$res_profile <- res_profile %>%
          relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
                     "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
                     "Start", "Stop", "Strand"))
        
        # Generate gene profile table
        output$gs_profile_table <- DT::renderDataTable(
          Screening$res_profile,
          selection = "single",
          rownames= FALSE,
          options = list(scrollX = TRUE,
                         autoWidth = TRUE,
                         pageLength = 10,  
                         columnDefs = list(list(searchable = TRUE, targets = "_all")),
                         columnDefs = list(list(width = '400px', targets = c("Sequence Name",
                                                                             "Name of Closest Sequence"))),
                         columnDefs = list(list(width = 'auto', targets = "_all")),
                         columnDefs = list(list(searchable = TRUE,
                                                targets = "_all")),
                         initComplete = DT::JS(
                           "function(settings, json) {",
                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '0px'});",
                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '0px'});",
                           "}"
                         ),
                         drawCallback = DT::JS(
                           "function(settings) {",
                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '0px'});",
                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '0px'});",
                           "}"
                         ))
        )
      } 
    } else {
      output$gs_profile_table <- NULL
    }
  })
  
  # Resistance profile selection table
  observe({
    req(DB$meta, DB$data, Screening$available)
    output$gs_isolate_table <- renderDataTable(
      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
      selection = "single",
      rownames= FALSE,
      options = list(pageLength = 10,
                     autoWidth = TRUE,
                     columnDefs = list(list(searchable = TRUE,
                                            targets = "_all",
                                            className = "dt-left")),
                     initComplete = DT::JS(
                       "function(settings, json) {",
                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                       "}"
                     ),
                     drawCallback = DT::JS(
                       "function(settings) {",
                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                       "}"
                     ))
    )
  })
  
  observeEvent(input$gs_table_view, {
    showModal(
      div(
        class = "start-modal",
        div(
          class = "modal-fit-content",
          modalDialog(
            fluidRow(
              fluidRow(
                br(), 
                column(
                  width = 11,
                  p(
                    HTML(
                      paste0(
                        '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                        "Click an isolate from the local database to display the corresponding gene screening results.",
                        '</span>'
                      )
                    )
                  ),
                  uiOutput("gs_table_selected_isolate")
                ),
                br()
              ),
              br(),
              column(
                width = 12,
                div(class = "loci_table",
                    dataTableOutput("gs_isolate_table"))
              ),
              br()
            ),
            title = paste("Select Isolate"),
            fade = TRUE,
            easyClose = TRUE,
            footer = tagList(
              modalButton("Dismiss"),
              actionButton("conf_gs_select", "Select")
            )
          )
        )
      )
    )
  })
  
  observeEvent(input$conf_gs_select, {
    meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
    selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
    
    updatePickerInput(session, "gs_profile_select",
                      selected = selected_isolate)
    
    removeModal()
  })
  
  observe({
    req(input$screening_res_sel, Startup$database, DB$scheme, DB$data, Screening$available)
    if(!is.null(Screening$status_df) &
       !is.null(input$screening_res_sel) & 
       !is.null(Screening$status_df$status) & 
       !is.null(Screening$status_df$isolate)) {
      if(length(input$screening_res_sel) > 0) {
        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
            results <- read.delim(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Isolates", 
                                            input$screening_res_sel, "amrfinder.out"))
            
            output$screening_table <- renderDataTable(
              select(results, c(6, 7, 8, 9, 11)),
              selection = "single",
              options = list(pageLength = 10,
                             columnDefs = list(list(searchable = TRUE,
                                                    targets = "_all")),
                             dom = "tip",
                             initComplete = DT::JS(
                               "function(settings, json) {",
                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             ),
                             drawCallback = DT::JS(
                               "function(settings) {",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             )))
          } else {output$screening_table <- NULL}
        }
      } else {
        output$screening_table <- NULL
      }
    } else {
      output$screening_table <- NULL
    }
    
  })
  
  # Availablity feedback
  output$gene_screening_info <- renderUI({
    req(DB$scheme)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    
    if(!isFALSE(amrfinder_available)) {
      p(
        HTML(
          paste(
            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
            DB$scheme, 'available for gene screening with ',
            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
            '</span>'
          )
        )
      )
    } else {
      p(
        HTML(
          paste(
            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
            DB$scheme, 'not available for gene screening with ',
            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
            '</span>'
          )
        )
      )
    }
  })
  
  output$gene_resistance_info <- renderUI({
    req(DB$scheme)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    
    if(!isFALSE(amrfinder_available)) {
      p(
        HTML(
          paste(
            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
            DB$scheme, 'available for gene screening with ',
            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
            '</span>'
          )
        )
      )
    } else {
      p(
        HTML(
          paste(
            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
            DB$scheme, 'not available for gene screening with ',
            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
            '</span>'
          )
        )
      )
    }
  })
  
  # Screening Interface
  
  output$screening_interface <- renderUI({
    req(DB$data, DB$scheme, Screening$available)
    amrfinder_available <- check.amrfinder.available(selected_scheme = DB$scheme,
                                                     amrfinder_species = amrfinder_species)
    
    if(!isFALSE(amrfinder_available)) {
      column(
        width = 12,
        fluidRow(
          column(1),
          column(
            width = 10,
            fluidRow(
              column(
                width = 3,
                align = "left",
                div(
                  class = "screening-box",
                  box(
                    solidHeader = TRUE,
                    status = "primary",
                    width = "100%",
                    title = "Initiate Screening",
                    column(
                      width = 12,
                      align = "center",
                      p(
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
                          )
                        )
                      ),
                      if(Screening$picker_status) {
                        div(
                          class = "screening_div",
                          pickerInput(
                            "screening_select",
                            "",
                            choices = list(
                              Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
                                as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
                              } else {
                                DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
                              },
                              Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
                                as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
                              } else {
                                DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
                              },
                              `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
                                as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
                              } else {
                                DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                              }
                            ),
                            choicesOpt = list(
                              disabled = c(
                                rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
                                rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
                                rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                              )
                            ),
                            options = list(
                              `live-search` = TRUE,
                              `actions-box` = TRUE,
                              size = 10,
                              style = "background-color: white; border-radius: 5px;"
                            ),
                            multiple = TRUE
                          )
                        )
                      } else {
                        div(
                          class = "screening_div",
                          pickerInput(
                            "screening_select",
                            "",
                            choices = Screening$picker_choices,
                            selected = Screening$picker_selected,
                            options = list(
                              `live-search` = TRUE,
                              `actions-box` = TRUE,
                              size = 10,
                              style = "background-color: white; border-radius: 5px;"
                            ),
                            multiple = TRUE
                          ) 
                        )
                      },
                      br(), br(),
                      uiOutput("genome_path_gs"),
                      br()
                    )
                  )
                )
              ),
              column(
                width = 3,
                uiOutput("screening_start")
              ),
              uiOutput("screening_result_sel")
            )    
          )
        ),
        fluidRow(
          column(1),
          column(
            width = 10,
            br(),  
            uiOutput("screening_result"),
            br(), br()
          )
        )
      )
    }
  })
  
  ### Screening Events ----
  
  output$download_resistance_profile <- downloadHandler(
    filename = function() {
      log_print(paste0("Save resistance profile table ", input$gs_profile_select, "_Profile.csv"))
      
      paste0(format(Sys.Date()), "_", input$gs_profile_select, "_Profile.csv")
    },
    content = function(file) {
      write.table(
        Screening$res_profile,
        file, 
        sep = ";",
        row.names = FALSE, 
        quote = FALSE
      ) 
    }
  )
  
  # Reset screening 
  observeEvent(input$screening_reset_bttn, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Reset gene screening")
    
    # reset status file
    sapply(Screening$status_df$isolate, remove.screening.status, 
           database = Startup$database, scheme = DB$scheme)
    
    # set feedback variables
    Screening$status <- "idle"
    Screening$status_df <- NULL
    Screening$choices <- NULL
    Screening$picker_status <- TRUE
    Screening$first_result <- NULL
    
    # change reactive UI
    output$screening_table <- NULL
    output$screening_result <- NULL
    output$screening_fail <- NULL
    
    updatePickerInput(session, "screening_select", selected = character(0))
    
    # enable isolate picker
    shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', false);"))
    shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Cancel screening
  observeEvent(input$screening_cancel, {
    showModal(
      div(
        class = "start-modal",
        modalDialog(
          fluidRow(
            br(), 
            column(
              width = 11,
              p(
                HTML(
                  paste0(
                    '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                    "Gene Screening still pending. Are you sure you want to stop the screening?",
                    '</span>'
                  )
                )
              )
            ),
            br()
          ),
          title = "Cancel Gene Screening",
          fade = TRUE,
          easyClose = TRUE,
          footer = tagList(
            modalButton("Cancel"),
            actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
          )
        )
      )
    )
  })
  
  observeEvent(input$conf_screening_cancel, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    log_print("Cancelled gene screening")
    removeModal()
    
    show_toast(
      title = "Gene Screening Terminated",
      type = "warning",
      position = "bottom-end",
      timer = 6000
    )
    
    # terminate screening
    system(paste0("kill $(pgrep -f 'bin/screening.sh')"), wait = FALSE)
    system(paste("killall -TERM tblastn"), wait = FALSE)
    
    # reset status file
    sapply(Screening$status_df$isolate, remove.screening.status, 
           database = Startup$database, scheme = DB$scheme)
    
    # set feedback variables
    Screening$status <- "idle"
    Screening$status_df <- NULL
    Screening$choices <- NULL
    Screening$picker_status <- TRUE
    Screening$first_result <- NULL
    
    # change reactive UI
    output$screening_table <- NULL
    output$screening_result <- NULL
    
    updatePickerInput(session, "screening_select", selected = character(0))
    
    # disable isolate picker
    shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', false);"))
    shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Get selected assembly
  observe({
    req(DB$data, Screening$status, Screening$available)
    if(length(input$screening_select) < 1) {
      output$genome_path_gs <- renderUI(HTML(
        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
      ))
      
      output$screening_start <- NULL
      
    } else if(length(input$screening_select) > 0) {
      
      output$screening_start <- renderUI({
        div(
          class = "screening-box",
          box(
            solidHeader = TRUE,
            status = "primary",
            width = "100%",
            title = "Perform Screening",
            if(length(input$screening_select) < 1) {
              column(
                width = 12,
                align = "center",
                p(
                  HTML(paste(
                    '<i class="fa-solid fa-circle-exclamation" style="font-size:16px;color:orange"></i>',
                    paste("<span style='color: white; font-style:italic'>", 
                          "&nbsp Select Isolate(s) for Screening")))
                ),
                br(),
                br()
              )
            } else if(Screening$status == "finished") {
              column(
                width = 12,
                align = "center",
                p(
                  HTML(paste(
                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
                    paste("<span style='color: white; font-style:italic'>", 
                          "&nbsp Reset to perform screening again")))
                ),
                fluidRow(
                  actionButton(
                    "screening_reset_bttn",
                    "Reset",
                    icon = icon("arrows-rotate")
                  )
                ),
                if(!is.null(Screening$status_df)) {
                  HTML(paste("<span style='color: white; font-style:italic;'>", 
                             sum(Screening$status_df$status != "unfinished"), "/",
                             nrow(Screening$status_df), " isolate(s) screened"))
                },
                br(),
                br()
              )
            } else if(Screening$status == "idle") {
              column(
                width = 12,
                align = "center",
                p(
                  HTML(paste(
                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
                    paste("<span style='color: white;font-size:15px'>",
                          "&nbsp Select isolates for screening")))
                ),
                actionButton(
                  inputId = "screening_start_button",
                  label = "Start",
                  icon = icon("circle-play")
                ),
                br(),
                br()
              )
            } else if(Screening$status == "started") {
              column(
                width = 12,
                align = "center",
                p(
                  HTML(paste(
                    '<i class="fa-solid fa-clock" style="font-size:16px;color:white"></i>',
                    paste("<span style='color: white;font-size:16px'>",
                          "&nbsp Running Screening ...")))
                ),
                fluidRow(
                  column(3),
                  column(
                    width = 3,
                    actionButton(
                      inputId = "screening_cancel",
                      label = "Terminate",
                      icon = icon("ban")
                    )
                  ),
                  column(
                    width = 3,
                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:35px; top:-10px"></i>'))
                  )
                ),
                if(!is.null(Screening$status_df)) {
                  HTML(paste("<span style='color: white; font-style:italic;'>", 
                             sum(Screening$status_df$status != "unfinished"), "/",
                             nrow(Screening$status_df), " isolate(s) screened"))
                },
                br(),
                br()
              )
            }
          )
        )
      })
    } else {NULL}
  })
  
  #### Running Screening ----
  
  observeEvent(input$screening_start_button, {
    
    if(tail(readLogFile(), 1) != "0") {
      show_toast(
        title = "Pending Multi Typing",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      
      log_print("Started gene screening")
      
      Screening$status <- "started"
      Screening$picker_choices <- list(
        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
        } else {
          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
        },
        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
        } else {
          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
        },
        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
        } else {
          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
        }
      )
      Screening$picker_selected <- input$screening_select
      Screening$picker_status <- FALSE
      
      show_toast(
        title = "Gene screening started",
        type = "success",
        position = "bottom-end",
        timer = 6000
      )
      
      Screening$meta_df <- data.frame(wd = getwd(),
                                      selected = paste(
                                        file.path(Startup$database, gsub(" ", "_", DB$scheme),
                                                  "Isolates", input$screening_select,
                                                  paste0(input$screening_select, ".zip")), 
                                        collapse = " "),
                                      species = gsub(" ", "_", check.amrfinder.available(
                                        selected_scheme = DB$scheme,
                                        amrfinder_species = amrfinder_species)),
                                      database = Startup$database,
                                      scheme = DB$scheme)
      
      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
                                        status = "unfinished")
      
      # Reset screening status
      sapply(Screening$status_df$isolate, remove.screening.status, 
             database = Startup$database, scheme = DB$scheme)
      
      saveRDS(Screening$meta_df, file.path(app_local_share_path, "screening_meta.rds"))
      
      # Disable pickerInput
      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
      
      # System execution screening.sh
      system(paste("bash", paste0(getwd(), "/bin/screening.sh")), wait = FALSE)
    }
  })
  
  observe({
    req(Screening$available, DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
    if(!is.null(Screening$status_df) &
       !is.null(Screening$status_df$status) & 
       !is.null(Screening$status_df$isolate) &
       !is.null(input$screening_res_sel)) {
      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
            output$screening_result <- renderUI(
              column(
                width = 12,
                p(
                  HTML(
                    paste(
                      '<i class="fa-solid fa-circle-check" style="font-size:16px;color:lightgreen"></i>',
                      paste("<span style='color: white; font-style:italic'>",
                            "&nbsp Results of gene screening appended to local database.")
                    )
                  )
                ),
                dataTableOutput("screening_table") 
              )
            )
          } else {
            output$screening_result <- renderUI(
              column(
                width = 12,
                br(),
                verbatimTextOutput("screening_fail")
              )
            )
          }
        }
      } else {
        output$screening_result <- NULL
      }
    } else {
      output$screening_result <- NULL
    }
  })
  
  observe({
    req(Screening$available, DB$data, Screening$status, input$screening_res_sel)
    if(!is.null(Screening$status_df) &
       !is.null(Screening$status_df$status) & 
       !is.null(Screening$status_df$isolate) &
       !is.null(input$screening_res_sel)) {
      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
            output$screening_fail <- renderPrint({
              cat(paste(readLines(file.path(Startup$database, gsub(" ", "_", DB$scheme),
                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
            })
          }
        }
      } else {
        output$screening_fail <- NULL
      }
    } else {
      output$screening_fail <- NULL
    }
  })
  
  observe({
    req(DB$data, Screening$available)
    if(!is.null(Screening$status)) {
      if(Screening$status != "idle") {
        
        # start status screening for user feedback
        check_screening()
        
        if(isTRUE(Screening$first_result)) {
          output$screening_result_sel <- renderUI(
            fluidRow(
              column(
                width = 2,
                align = "center",
                HTML('<i class="fa-solid fa-right-long fa-beat-fade" style="font-size: 50px; color: white; margin-top: 80px;"></i>')
              ),
              column(
                width = 3,
                align = "left",
                div(
                  class = "screening-box",
                  box(
                    solidHeader = TRUE,
                    status = "primary",
                    width = "100%",
                    title = "Browse Result(s)",
                    column(
                      width = 12,
                      align = "center",
                      p(
                        HTML(
                          paste(
                            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select screening results')
                          )
                        )
                      ),
                      div(
                        class = "screening-div",
                        selectInput(
                          "screening_res_sel",
                          label = "",
                          choices = ""
                        )
                      ),
                      if(!is.null(Screening$status_df)) {
                        HTML(paste("<span style='color: white; font-style:italic;'>", 
                                   if(sum(Screening$status_df$status == "success") == 1) {
                                     "1 success &nbsp / &nbsp"
                                   } else {
                                     paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
                                   },
                                   if(sum(Screening$status_df$status == "fail") == 1) {
                                     "1 failure"
                                   } else {
                                     paste0(sum(Screening$status_df$status == "fail"), " failures")
                                   }))
                      }, 
                      br(), br()
                    )
                  )
                )   
              )
            )
          )
          
          Screening$first_result <- FALSE
        }
      } else if(Screening$status == "idle") {
        output$screening_result_sel <- NULL
      }
    }
  }) 
  
  check_screening <- reactive({
    invalidateLater(500, session)
    
    req(Screening$status_df)
    
    if(Screening$status == "started") {
      
      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status, 
                                           database = Startup$database, scheme = DB$scheme)
      
      if(any("unfinished" != Screening$status_df$status) &
         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
        
        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
        
        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
                                                                 Screening$status_df$status == "fail")]
        
        if(sum(Screening$status_df$status != "unfinished") > 0) {
          if(is.null(Screening$first_result)) {
            Screening$first_result <- TRUE
          }
        }
        
        if(tail(status_df$status, 1) == "success") {
          
          # Changing "Screened" metadata variable in database
          Database <- readRDS(file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
          
          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
          
          saveRDS(Database, file.path(Startup$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
          
          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
          
          DB$meta_gs <- select(DB$data, c(1, 3:13))
          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
          
          show_toast(
            title = paste("Successful screening of", tail(Screening$choices, 1)),
            type = "success",
            position = "bottom-end",
            timer = 6000)
          
          updateSelectInput(session = session,
                            inputId = "screening_res_sel",
                            choices = Screening$choices,
                            selected = tail(Screening$choices, 1))
          
          # Disable pickerInput
          shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
          shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
          
        } else if(tail(status_df$status, 1) == "fail") {
          
          show_toast(
            title = paste("Failed screening of", tail(status_df$isolate, 1)),
            type = "error",
            position = "bottom-end",
            timer = 6000)
          
          updateSelectInput(session = session,
                            inputId = "screening_res_sel",
                            choices = Screening$choices,
                            selected = tail(Screening$choices, 1))
          
          # Disable pickerInput
          shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
          shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
        }
        
        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
          Screening$status <- "finished"
        }
      } else {
        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
          Screening$status <- "finished"
        }
      }
      
      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
        Screening$status <- "finished"
      }
    }
  }) 
  
  ### AMR Visualization ----
  
  gs_plot_selected_isolate <- reactiveVal()
  gs_plot_selected_amr <- reactiveVal()
  gs_plot_selected_vir <- reactiveVal()
  gs_plot_selected_noclass <- reactiveVal()
  
  observe({
    if(!is.null(input$gs_plot_selected_isolate)) {
      gs_plot_selected_isolate(input$gs_plot_selected_isolate)
    }
    if(!is.null(input$gs_plot_selected_amr)) {
      gs_plot_selected_amr(input$gs_plot_selected_amr)
    } else {
      gs_plot_selected_amr(character(0))
    }
    if(!is.null(input$gs_plot_selected_vir)) {
      gs_plot_selected_vir(input$gs_plot_selected_vir)
    } else {
      gs_plot_selected_vir(character(0))
    }
    if(!is.null(input$gs_plot_selected_noclass)) {
      gs_plot_selected_noclass(input$gs_plot_selected_noclass)
    } else {
      gs_plot_selected_noclass(character(0))
    }
  })
  
  gs_virclass_scale <- reactiveVal()
  gs_amrclass_scale <- reactiveVal()
  gs_amr_variables <- reactiveVal()
  gs_vir_variables <- reactiveVal()
  gs_mapping_scale <- reactiveVal()
  gs_var_mapping <- reactiveVal()
  
  observe({
    if (!is.null(input$gs_virclass_scale)) {
      gs_virclass_scale(input$gs_virclass_scale)
    }
    
    if (!is.null(input$gs_amrclass_scale)) {
      gs_amrclass_scale(input$gs_amrclass_scale)
    }
    
    if (!is.null(input$gs_vir_variables)) {
      gs_vir_variables(input$gs_vir_variables)
    }
    
    if (!is.null(input$gs_amr_variables)) {
      gs_amr_variables(input$gs_amr_variables)
    }
    
    if (!is.null(input$gs_var_mapping)) {
      gs_var_mapping(input$gs_var_mapping)
    }
    
    if (!is.null(input$gs_mapping_scale)) {
      gs_mapping_scale(input$gs_mapping_scale)
    }
  })
  
  gsplot_color_text <- reactiveVal()
  gsplot_color_dend <- reactiveVal()
  gsplot_color_palette1 <- reactiveVal()
  gsplot_color_palette2 <- reactiveVal()
  gsplot_grid_color <- reactiveVal()
  gsplot_background <- reactiveVal()
  
  observe({
    if (!is.null(input$gsplot_color_text)) {
      gsplot_color_text(input$gsplot_color_text)
    }
    if (!is.null(input$gsplot_color_dend)) {
      gsplot_color_dend(input$gsplot_color_dend)
    }
    if (!is.null(input$gsplot_color_palette1)) {
      gsplot_color_palette1(input$gsplot_color_palette1)
    }
    if (!is.null(input$gsplot_color_palette2)) {
      gsplot_color_palette2(input$gsplot_color_palette2)
    }
    if (!is.null(input$gsplot_grid_color)) {
      gsplot_grid_color(input$gsplot_grid_color)
    }
    if (!is.null(input$gsplot_background)) {
      gsplot_background(input$gsplot_background)
    }
  })
  
  gs_plot <- reactive({
    req(DB$data, Screening$amr_results, Startup$database, DB$scheme)
    
    # get inputs
    if(!is.null(input$gs_plot_selected_isolate)) {
      gs_plot_selected_isolate <- input$gs_plot_selected_isolate
    } else {
      gs_plot_selected_isolate <- DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
    }
    
    if(length(gs_plot_selected_isolate) > 2) {
      gs_plot_selected_amr <- input$gs_plot_selected_amr
      gs_plot_selected_vir <- input$gs_plot_selected_vir
      gs_plot_selected_noclass <- input$gs_plot_selected_noclass
      
      # get heatmap 
      amr_profile_numeric <- as.data.frame(lapply(Screening$amr_results, as.numeric))
      rownames(amr_profile_numeric) <- rownames(Screening$amr_results)
      colnames(amr_profile_numeric) <- colnames(Screening$amr_results)
      
      if((length(c(gs_plot_selected_amr, gs_plot_selected_vir, gs_plot_selected_noclass)) >= 3) & (length(gs_plot_selected_isolate) >= 3)) {
        
        ### get heatmap meta
        amr_profile_numeric_all <- amr_profile_numeric[rownames(amr_profile_numeric) %in% gs_plot_selected_isolate, ]
        amr_profile_numeric <- amr_profile_numeric_all[,c(gs_plot_selected_amr, gs_plot_selected_vir, gs_plot_selected_noclass)]
        heatmap_mat <- as.matrix(amr_profile_numeric)
        
        # metadata
        amr_meta <- get.gsMeta(gene_class = Screening$amr_class, hm_matrix = heatmap_mat)
        colnames(amr_meta) <- "amr"
        vir_meta <- get.gsMeta(gene_class = Screening$vir_class, hm_matrix = heatmap_mat)
        
        # unite meta
        Screening$hm_meta <- add_column(amr_meta, vir = vir_meta$class)
        hm_meta <- Screening$hm_meta
        
        # styling parameters
        ht_opt$ANNOTATION_LEGEND_PADDING = unit(10, "mm")
        ht_opt$HEATMAP_LEGEND_PADDING = unit(5, "mm")
        
        if(!is.null(input$gsplot_isolate_label)) {
          gsplot_isolate_label <- input$gsplot_isolate_label
        } else {
          gsplot_isolate_label <- "Assembly Name"
        }
        
        if(!is.null(input$gsplot_color_text)) {
          gsplot_color_text <- input$gsplot_color_text
        } else if(is.null(gsplot_color_text())){
          gsplot_color_text <- "#000000"
        } else {
          gsplot_color_text <- gsplot_color_text()
        }
        
        if(!is.null(input$gsplot_treeheight_col)) {
          gsplot_treeheight_col <- input$gsplot_treeheight_col
        } else {
          gsplot_treeheight_col <- 2
        }
        
        if(!is.null(input$gsplot_treeheight_row)) {
          gsplot_treeheight_row <- input$gsplot_treeheight_row
        } else {
          gsplot_treeheight_row <- 2
        }
        
        if(!is.null(input$gsplot_legend_labelsize)) {
          gsplot_legend_labelsize <- input$gsplot_legend_labelsize
        } else {
          gsplot_legend_labelsize <- 9
        }
        
        if(!is.null(input$gsplot_color_palette1)) {
          gsplot_color_palette1 <- input$gsplot_color_palette1
        } else {
          gsplot_color_palette1 <- "#66C2A5"
        }
        
        if(!is.null(input$gsplot_color_palette2)) {
          gsplot_color_palette2 <- input$gsplot_color_palette2
        } else {
          gsplot_color_palette2 <- "#E5C494"
        }
        
        if(!is.null(input$gs_amr_variables)) {
          gs_amr_variables <- input$gs_amr_variables
        } else {
          gs_amr_variables <- "Classification"
        }
        
        if(!is.null(input$gs_vir_variables)) {
          gs_vir_variables <- input$gs_vir_variables
        } else {
          gs_vir_variables <- "Classification"
        }
        
        if(!is.null(input$gsplot_grid_color)) {
          gsplot_grid_color <- input$gsplot_grid_color
        } else {
          gsplot_grid_color <- "#FFFFFF"
        }
        
        if(!is.null(input$gsplot_grid_width)) {
          gsplot_grid_width <- input$gsplot_grid_width
        } else {
          gsplot_grid_width <- 1
        }
        
        if(!is.null(input$gsplot_fontsize_title)) {
          gsplot_fontsize_title <- input$gsplot_fontsize_title
        } else {
          gsplot_fontsize_title <- 16
        }
        
        if(!is.null(input$gs_cluster_col)) {
          gs_cluster_col <- input$gs_cluster_col
        } else {
          gs_cluster_col <- TRUE
        }
        
        if(!is.null(input$gs_cluster_distance_col)) {
          if(input$gs_cluster_distance_col == "binary") {
            gs_cluster_distance_col <- "binary"
          } else if(input$gs_cluster_distance_col == "mcc") {
            gs_cluster_distance_col <- function(m) mcc_dist_matrix(m)
          } else if(input$gs_cluster_distance_col == "hamming") {
            gs_cluster_distance_col <- function(m) hamming_dist_matrix(m)
          }
        } else {
          gs_cluster_distance_col <- "binary"
        }
        
        if(!is.null(input$gs_cluster_method_col)) {
          gs_cluster_method_col <- input$gs_cluster_method_col
        } else {
          gs_cluster_method_col <- "average"
        }
        
        if(!is.null(input$gs_cluster_row)) {
          gs_cluster_row <- input$gs_cluster_row
        } else {
          gs_cluster_row <- TRUE
        }
        
        if(!is.null(input$gs_cluster_distance_row)) {
          if(input$gs_cluster_distance_row == "binary") {
            gs_cluster_distance_row <- "binary"
          } else if(input$gs_cluster_distance_row == "mcc") {
            gs_cluster_distance_row <- function(m) mcc_dist_matrix(m)
          } else if(input$gs_cluster_distance_row == "hamming") {
            gs_cluster_distance_row <- function(m) hamming_dist_matrix(m)
          }
        } else {
          gs_cluster_distance_row <- "binary"
        }
        
        if(!is.null(input$gs_cluster_method_row)) {
          gs_cluster_method_row <- input$gs_cluster_method_row
        } else {
          gs_cluster_method_row <- "average"
        }
        
        if(!is.null(input$gsplot_color_dend)) {
          gsplot_color_dend <- input$gsplot_color_dend
        } else {
          gsplot_color_dend <- "#000000"
        }
        
        if(!is.null(input$gsplot_background)) {
          gsplot_background <- input$gsplot_background
        } else {
          gsplot_background <- "#FFFFFF"
        }
        
        legend_gp <- gpar(col = gsplot_color_text,
                          fill = c(gsplot_color_palette1, gsplot_color_palette2))
        labels_gp <- gpar(col = gsplot_color_text,
                          fontsize = gsplot_legend_labelsize)
        title_gp <- gpar(col = gsplot_color_text,
                         fontsize = gsplot_legend_labelsize + 2)
        grid_height <- unit(gsplot_legend_labelsize * 0.8, "mm")
        grid_width <- unit(gsplot_legend_labelsize * 0.8, "mm")
        
        if(length(gs_plot_selected_isolate) < 10){
          fontsize_row <- 14
        } else if(length(gs_plot_selected_isolate) < 20){
          fontsize_row <- 12
        } else if(length(gs_plot_selected_isolate) < 30){
          fontsize_row <- 11
        } else if(length(gs_plot_selected_isolate) < 50){
          fontsize_row <- 10
        } else if(length(gs_plot_selected_isolate) < 80){
          fontsize_row <- 9
        } else if(length(gs_plot_selected_isolate) < 120){
          fontsize_row <- 8
        } else if(length(gs_plot_selected_isolate) < 160){
          fontsize_row <- 7
        } else if(length(gs_plot_selected_isolate) < 200){
          fontsize_row <- 6
        } else {
          fontsize_row <- 5
        } 
        
        col_count <- length(c(gs_plot_selected_amr, 
                              gs_plot_selected_vir, 
                              gs_plot_selected_noclass))
        if(col_count < 10){
          fontsize_col <- 15
        } else if(col_count < 20){
          fontsize_col <- 13
        } else if(col_count < 30){
          fontsize_col <- 12
        } else if(col_count < 50){
          fontsize_col <- 10
        } else if(col_count < 80){
          fontsize_col <- 9
        } else if(col_count < 120){
          fontsize_col <- 8
        } else if(col_count < 160){
          fontsize_col <- 7
        } else if(col_count < 200){
          fontsize_col <- 6
        } else {
          fontsize_col <- 5
        } 
        
        fontsize_legend <- 2
        
        if(isTRUE(gs_cluster_row)) {
          row_order <- NULL
        } else {
          row_order <- rownames(heatmap_mat)
        }
        
        amr_order <- sort(arrange(hm_meta, amr))
        column_order_amr <- rownames(amr_order)[!is.na(amr_order$amr)]
        vir_order <- sort(arrange(hm_meta, vir))
        column_order_vir <- rownames(vir_order)[!is.na(vir_order$vir)]
        
        # heatmap annotations
        if(!is.null(input$gs_var_mapping)) {
          gs_var_mapping <- input$gs_var_mapping
        } else {
          gs_var_mapping <- "None"
        }
        
        isolate_annotation <- NULL
        isolate_annotation_legend <- NULL
        if(!is.null(input$gs_var_mapping)) {
          if(gs_var_mapping != "None") {
            
            isolate_meta <- DB$meta[which(DB$meta$`Assembly ID` %in% rownames(heatmap_mat)),]
            
            rownames(isolate_meta) <- rownames(heatmap_mat)
            
            sel_isolate_var <- isolate_meta[[gs_var_mapping]]
            dist_col <- length(unique(sel_isolate_var))
            if(all(sel_isolate_var == "")) {
              var_colors <- "grey"
              names(var_colors) <- "NA"
            } else {
              if(!is.null(input$gs_mapping_scale)) {
                if(input$gs_mapping_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
                  var_colors <- get(input$gs_mapping_scale)(dist_col)
                } else {
                  if(dist_col < 3) {
                    var_colors <- brewer.pal(3, input$gs_mapping_scale)[1:dist_col]
                  } else {
                    var_colors <- brewer.pal(dist_col, input$gs_mapping_scale)    
                  }
                }
              } else {
                var_colors <- get("viridis")(dist_col)
              }
              names(var_colors) <- unique(sort(sel_isolate_var))
            }
            
            isolate_annotation <- HeatmapAnnotation(
              Var = sel_isolate_var,
              show_legend = FALSE,
              col = list(Var = var_colors),  
              show_annotation_name = TRUE,
              annotation_label = gs_var_mapping,
              annotation_name_gp = gpar(col = gsplot_color_text),
              which = "row"
            )
            
            isolate_annotation_legend <- packLegend(
              Legend(
                at = names(var_colors),
                labels = names(var_colors),
                title = gs_var_mapping,
                labels_gp = labels_gp,
                title_gp = title_gp,
                grid_height = grid_height,
                grid_width = grid_width,
                legend_gp = gpar(fill = var_colors)
              )
            )
          }  
        }
        
        amr_annotation <- NULL
        amr_heatmap <- NULL
        sel_amr <- NULL
        if(!is.null(gs_plot_selected_amr)) {
          if(all(is.na(hm_meta$amr)) | length(gs_plot_selected_amr) < 3) {
            amr_annotation <- NULL
            amr_heatmap <- NULL
          } else {
            if(gs_amr_variables != "None") {
              sel_amr <- amr_order$amr[!is.na(amr_order$amr)]
              dist_col <- length(unique(sel_amr))
              
              if(!is.null(input$gs_amrclass_scale)) {
                if(input$gs_amrclass_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
                  amr_colors <- get(input$gs_amrclass_scale)(length(unique(sel_amr)))
                } else {
                  if(dist_col < 3) {
                    amr_colors <- brewer.pal(3, input$gs_amrclass_scale)[1:dist_col]
                  } else {
                    amr_colors <- brewer.pal(dist_col, input$gs_amrclass_scale)    
                  }
                }
              } else {
                if(length(unique(Screening$hm_meta$amr)) > 7) {
                  amr_colors <- get("turbo")(length(unique(sel_amr)))
                } else {
                  if(dist_col < 3) {
                    amr_colors <- brewer.pal(3, "Set1")[1:dist_col]
                  } else {
                    amr_colors <- brewer.pal(dist_col, "Set1")    
                  }
                }
              }
              names(amr_colors) <- unique(sel_amr)
              
              amr_annotation <- HeatmapAnnotation(
                AMR = sel_amr,
                show_legend = TRUE,
                col = list(AMR = amr_colors),  
                show_annotation_name = FALSE,
                annotation_legend_param = list(
                  title = "AMR",
                  labels_gp = labels_gp,
                  title_gp = title_gp,
                  grid_height = grid_height,
                  grid_width = grid_width,
                  legend_gp = gpar(fill = amr_colors) 
                )
              )
            }
            
            # AMR heatmap
            amr_profile_matrix <- NULL
            amr_genes <- rownames(hm_meta)[!is.na(hm_meta$amr)]
            amr_profile_matrix_unordered <- heatmap_mat[,colnames(heatmap_mat) %in% amr_genes]
            amr_profile_matrix <- amr_profile_matrix_unordered[,c(column_order_amr)]
            
            if((all(amr_profile_matrix == 0)) | all(amr_profile_matrix == 1)) {
              amr_cols <- gsplot_color_palette1
            } else {
              amr_cols <- c(gsplot_color_palette1, gsplot_color_palette2)
            }
            
            amr_heatmap <- ComplexHeatmap::Heatmap(
              amr_profile_matrix,
              col = amr_cols,
              rect_gp = gpar(col = gsplot_grid_color, lwd = gsplot_grid_width),
              column_title = "AMR",
              column_title_gp = gpar(col = gsplot_color_text,
                                     fontsize = gsplot_fontsize_title),
              row_title = "Isolates",
              row_title_gp = gpar(col = gsplot_color_text,
                                  fontsize = gsplot_fontsize_title),
              row_names_gp = gpar(fontsize = fontsize_row, 
                                  col = gsplot_color_text),
              column_names_gp = gpar(fontsize = fontsize_col, 
                                     col = gsplot_color_text),
              cluster_columns = gs_cluster_col,
              clustering_distance_columns = gs_cluster_distance_col,
              clustering_method_columns = gs_cluster_method_col,
              cluster_rows = gs_cluster_row,
              clustering_distance_rows = gs_cluster_distance_row,
              clustering_method_rows = gs_cluster_method_row,
              column_dend_height = unit(gsplot_treeheight_col, "cm"), 
              row_dend_width = unit(gsplot_treeheight_row, "cm"),
              row_dend_gp = gpar(col = gsplot_color_dend),    
              column_dend_gp = gpar(col = gsplot_color_dend), 
              top_annotation = amr_annotation,
              show_heatmap_legend = FALSE,
              left_annotation = isolate_annotation,
              row_order = row_order,
              row_labels = DB$data[c(gsplot_isolate_label)][which(DB$data$`Assembly ID` %in% rownames(amr_profile_matrix)),]
            )
          }
        } else {
          amr_annotation <- NULL
          amr_heatmap <- NULL
        }
        
        vir_annotation <- NULL
        vir_heatmap <- NULL
        if(!is.null(gs_plot_selected_vir)) {
          if(all(is.na(hm_meta$vir)) | length(gs_plot_selected_vir) < 3) {
            vir_annotation <- NULL
            vir_heatmap <- NULL
          } else {
            if(gs_vir_variables != "None") {
              
              sel_vir <- vir_order$vir[!is.na(vir_order$vir)]
              dist_col <- length(unique(sel_vir))
              
              if(!is.null(input$gs_virclass_scale)) {
                
                if(input$gs_virclass_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
                  vir_colors <- get(input$gs_virclass_scale)(length(unique(sel_vir)))
                } else {
                  if(dist_col < 3) {
                    vir_colors <- brewer.pal(3, input$gs_virclass_scale)[1:dist_col]
                  } else {
                    vir_colors <- brewer.pal(dist_col, input$gs_virclass_scale)    
                  }
                }
              } else {
                if(length(unique(Screening$hm_meta$vir)) > 7) {
                  vir_colors <- get("turbo")(length(unique(sel_vir)))
                } else {
                  if(dist_col < 3) {
                    vir_colors <- brewer.pal(3, "Set1")[1:dist_col]
                  } else {
                    vir_colors <- brewer.pal(dist_col, "Set1")    
                  }
                }
              }
              names(vir_colors) <- unique(sel_vir)
              
              vir_annotation <- HeatmapAnnotation(
                Vir = sel_vir,
                show_legend = TRUE,
                col = list(Vir = vir_colors),  
                show_annotation_name = FALSE,
                annotation_legend_param = list(
                  title = "Virulence",
                  legend_gp = legend_gp,
                  labels_gp = labels_gp,
                  title_gp = title_gp,
                  grid_height = grid_height,
                  grid_width = grid_width,
                  legend_gp = gpar(fill = vir_colors) 
                )
              )
            }
            
            # Vir heatmap
            vir_profile_matrix <- NULL
            vir_genes <- rownames(hm_meta)[!is.na(hm_meta$vir)]
            vir_profile_matrix <- heatmap_mat[,colnames(heatmap_mat) %in% vir_genes]
            vir_profile_matrix_unordered <- heatmap_mat[,colnames(heatmap_mat) %in% vir_genes]
            vir_profile_matrix <- vir_profile_matrix_unordered[,c(column_order_vir)]
            
            if((all(vir_profile_matrix == 0)) | all(vir_profile_matrix == 1)) {
              vir_cols <- gsplot_color_palette1
            } else {
              vir_cols <- c(gsplot_color_palette1, gsplot_color_palette2)
            }
            
            if(all(is.na(hm_meta$amr)) | length(gs_plot_selected_amr) < 3) {
              left_annotation <- isolate_annotation
            }  else {
              left_annotation <- NULL
            }
            
            vir_heatmap <- ComplexHeatmap::Heatmap(
              vir_profile_matrix,
              col = vir_cols,
              rect_gp = gpar(col = gsplot_grid_color, lwd = gsplot_grid_width),
              column_title = "Virulence",
              column_title_gp = gpar(col = gsplot_color_text,
                                     fontsize = gsplot_fontsize_title),
              row_title = "Isolates",
              row_title_gp = gpar(col = gsplot_color_text,
                                  fontsize = gsplot_fontsize_title),
              row_names_gp = gpar(fontsize = fontsize_row, 
                                  col = gsplot_color_text),
              column_names_gp = gpar(fontsize = fontsize_col, 
                                     col = gsplot_color_text),
              column_dend_height = unit(gsplot_treeheight_col, "cm"), 
              cluster_columns = gs_cluster_col,
              clustering_distance_columns = gs_cluster_distance_col,
              clustering_method_columns = gs_cluster_method_col,
              cluster_rows = gs_cluster_row,
              row_order = row_order,
              clustering_distance_rows = gs_cluster_distance_row,
              clustering_method_rows = gs_cluster_method_row,
              row_dend_width = unit(gsplot_treeheight_row, "cm"),
              row_dend_gp = gpar(col = gsplot_color_dend),    
              column_dend_gp = gpar(col = gsplot_color_dend), 
              top_annotation = vir_annotation,
              show_heatmap_legend = FALSE,
              left_annotation = left_annotation,
              row_labels = DB$data[c(gsplot_isolate_label)][which(DB$data$`Assembly ID` %in% rownames(vir_profile_matrix)),]
            )
          }
        } else {
          vir_annotation <- NULL
          vir_heatmap <- NULL
        } 
        
        # None heatmap
        noclass_heatmap <- NULL
        noclass_profile_matrix <- NULL
        if(!is.null(gs_plot_selected_noclass)) {
          if(any(is.na(hm_meta$vir) & is.na(hm_meta$amr))) {
            unclass_genes <- rownames(hm_meta)[is.na(hm_meta$vir) & is.na(hm_meta$amr)]
            noclass_profile_matrix <- heatmap_mat[,colnames(heatmap_mat) %in% unclass_genes]
            
            if((all(is.na(hm_meta$amr)) | length(gs_plot_selected_amr) < 3) & (all(is.na(hm_meta$vir)) | length(gs_plot_selected_vir) < 3)) {
              left_annotation <- isolate_annotation
            } else {
              left_annotation <- NULL
            }
            
            if((all(noclass_profile_matrix == 0)) | all(noclass_profile_matrix == 1)) {
              noclass_cols <- gsplot_color_palette1
            } else {
              noclass_cols <- c(gsplot_color_palette1, gsplot_color_palette2)
            }
            
            noclass_heatmap <- ComplexHeatmap::Heatmap(
              noclass_profile_matrix,
              col = noclass_cols,
              rect_gp = gpar(col = gsplot_grid_color, lwd = gsplot_grid_width),
              row_title = "Isolates",
              row_title_gp = gpar(col = gsplot_color_text,
                                  fontsize = gsplot_fontsize_title),
              row_names_gp = gpar(fontsize = fontsize_row, 
                                  col = gsplot_color_text),
              column_names_gp = gpar(fontsize = fontsize_col, 
                                     col = gsplot_color_text),
              column_dend_height = unit(gsplot_treeheight_col, "cm"), 
              cluster_columns = gs_cluster_col,
              clustering_distance_columns = gs_cluster_distance_col,
              clustering_method_columns = gs_cluster_method_col,
              cluster_rows = gs_cluster_row,
              row_order = row_order,
              clustering_distance_rows = gs_cluster_distance_row,
              clustering_method_rows = gs_cluster_method_row,
              row_dend_width = unit(gsplot_treeheight_row, "cm"),
              row_dend_gp = gpar(col = gsplot_color_dend),    
              column_dend_gp = gpar(col = gsplot_color_dend),
              show_heatmap_legend = FALSE,
              left_annotation = left_annotation,
              row_labels = DB$data[c(gsplot_isolate_label)][which(DB$data$`Assembly ID` %in% rownames(noclass_profile_matrix)),]
            )
          } else {
            noclass_heatmap <- NULL
          }
        } else {
          noclass_heatmap <- NULL
        }
        
        # custom legend
        custom_legend <- packLegend(
          Legend(
            labels = c("Present", "Absent"),
            title = "Gene Presence",
            legend_gp = gpar(col = gsplot_color_text,
                             fill = c(gsplot_color_palette1, gsplot_color_palette2)),
            labels_gp = gpar(col = gsplot_color_text,
                             fontsize = gsplot_legend_labelsize + 1),
            title_gp = gpar(col = gsplot_color_text,
                            fontsize = gsplot_legend_labelsize + 3,
                            fontface = "bold"),
            grid_height = unit((gsplot_legend_labelsize + 1) * 0.8, "mm"),
            grid_width = unit((gsplot_legend_labelsize + 1) * 0.8, "mm"),
            at = c(1, 0),
            nrow = 1,
            direction = "horizontal",
            title_position = "lefttop"
          )
        )
        
        # summarize heatmaps
        if(is.null(amr_heatmap) & is.null(vir_heatmap) & is.null(noclass_heatmap)) {
          output$gs_plot <- NULL
        } else {
          
          if(!is.null(amr_heatmap) & !is.null(vir_heatmap) & !is.null(noclass_heatmap)) {
            heatmaps <- amr_heatmap + vir_heatmap + noclass_heatmap
          } else if(!is.null(amr_heatmap) & !is.null(vir_heatmap) & is.null(noclass_heatmap)) {
            heatmaps <- amr_heatmap + vir_heatmap
          } else if(!is.null(amr_heatmap) & is.null(vir_heatmap) & !is.null(noclass_heatmap)) {
            heatmaps <- amr_heatmap + noclass_heatmap
          } else if(is.null(amr_heatmap) & !is.null(vir_heatmap) & !is.null(noclass_heatmap)) {
            heatmaps <- vir_heatmap + noclass_heatmap
          } else if(is.null(amr_heatmap) & is.null(vir_heatmap) & !is.null(noclass_heatmap)) {
            heatmaps <- noclass_heatmap
          } else if(!is.null(amr_heatmap) & is.null(vir_heatmap) & is.null(noclass_heatmap)) {
            heatmaps <- amr_heatmap
          } else if(is.null(amr_heatmap) & !is.null(vir_heatmap) & is.null(noclass_heatmap)) {
            heatmaps <- vir_heatmap
          }
          
          if(is.null(isolate_annotation_legend)) {
            
            ComplexHeatmap::draw(
              heatmaps,
              background = gsplot_background,
              heatmap_legend_list = custom_legend,
              heatmap_legend_side = "bottom",
              padding = unit(c(2, 2, 2, 2), "mm")
            )
          } else {
            ComplexHeatmap::draw(
              heatmaps,
              background = gsplot_background,
              heatmap_legend_list = custom_legend,
              heatmap_legend_side = "bottom",
              annotation_legend_list = isolate_annotation_legend,
              annotation_legend_side = "right"
            )
          }
        }
      } 
    } else {
      NULL
    }
  })
  
  # make plot
  output$gs_plot <- renderPlot({
    gs_plot()
  })
  
  # _______________________ ####
  
  ## Typing  ----
  
  # Render Single/Multi Switch
  
  readLogFile <- reactive({
    invalidateLater(5000, session)
    readLines(file.path(logdir, "script_log.txt"))
  })
  
  # No db typing message
  output$typing_no_db <- renderUI({
    if(!is.null(DB$exist)) {
      if(DB$exist) {
        column(
          width = 4,
          align = "left",
          br(),
          br(),
          br(),
          br(),
          p(
            HTML(
              paste0(
                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 50px', 'To initiate allelic typing, a cgMLST scheme must be downloaded first.'
                )
              )
            )
          )
        )
      } else {NULL}
    } else {NULL}
  })
  
  ### Typing UI Elements ----
  output$initiate_multi_typing_ui <- initiate_multi_typing_ui
  
  # Render selection info
  output$multi_folder_sel_info <- renderUI({
    
    req(Typing$assembly_folder_path, Typing$file_selection)
    
    if(Typing$file_selection == "folder") {
      if(length(Typing$assembly_folder_path) < 1) {
        HTML(paste("<span style='color: white; position:relative; top:8px; font-style: italic'>", 
                   "No files selected"))
      } else {
        HTML(paste("<span style='color: white; position:relative; top:8px; font-style: italic'>",
                   '<i class="fa-solid fa-arrow-right" style="font-size:15px;color:white"></i>',
                   "&nbsp",
                   length(Typing$files_filtered),
                   if(length(Typing$files_filtered) == 1) {
                     " file selected"
                   } else {" files selected"}))
      }
    } else {NULL}
  })
  
  output$multi_file_sel_info <- renderUI({
    
    req(Typing$assembly_files_path, Typing$file_selection)
    
    if(Typing$file_selection == "files") {
      if(nrow(Typing$assembly_files_path) < 1) {
        HTML(paste("<span style='color: white; position:relative; top:7px; font-style: italic'>", 
                   "No files selected"))
      } else {
        HTML(paste("<span style='color: white; position:relative; top:7px; font-style: italic'>",
                   '<i class="fa-solid fa-arrow-right" style="font-size:15px;color:white"></i>',
                   "&nbsp",
                   length(Typing$files_filtered),
                   if(length(Typing$files_filtered) == 1) {
                     " file selected"
                   } else {" files selected"}))
      }
    } else {NULL}
  })
  
  # Render multi selection table issues
  output$multi_select_issues <- renderUI({
    
    req(Typing$multi_sel_table, input$multi_select_table)
    
    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
      HTML(
        paste(
          paste("<span style='color: orange; position:relative; top:2px'>",
                "Some name(s) are already present in local database<br/>"),
          paste("<span style='color: #ff7334;'>",
                "Duplicated name(s). <br/>")
        )
      )
    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
      HTML(
        paste("<span style='color: #e0b300; position:relative; top:2px'>",
              "Some name(s) are already present in local database<br/>")
      )
    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
      HTML(
        paste("<span style='color: #ff7334; position:relative; top:2px'>",
              "Duplicated name(s) <br/>")
      )
    }
  })
  
  output$multi_select_issue_info <- renderUI({
    req(Typing$multi_sel_table, input$multi_select_table)
    
    multi_select_table <- hot_to_r(input$multi_select_table)
    
    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
      
      shinyjs::disable("conf_meta_multi")
      
      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
        
        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
          HTML(paste(
            paste(
              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
              paste("<span style='color: white; font-style:italic'>",
                    "&nbspRename highlighted isolates or deselect them</br>")),
            paste(
              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
              paste("<span style='color: white; font-style:italic'>",
                    "&nbspFilename(s) contain(s) empty spaces"))
          ))
        } else {
          HTML(paste(
            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
            paste("<span style='color: white; font-style:italic'>",
                  "&nbspFilename(s) contain(s) empty spaces")))
        }
      } else {
        HTML(paste(
          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
          paste("<span style='color: white; font-style:italic'>", 
                "&nbspRename highlighted isolates or deselect them")))
      }
    } else {
      shinyjs::enable("conf_meta_multi")
      HTML(paste(
        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
        paste("<span style='color: white; font-style:italic'>",
              "&nbspFiles ready for allelic typing")))
    }
  })
  
  # Render Metadata Select Box after Folder selection
  observe({
    if(!is.null(Typing$multi_sel_table)) {
      if (nrow(Typing$multi_sel_table) > 0) {
        
        output$multi_select_tab_ctrls <- renderUI(
          fluidRow(
            h3(p("Metadata Declaration"), style = "color:white; margin-left: 15px"),
            br(),
            column(
              width = 1,
              align = "left",
              actionButton(
                "sel_all_mt",
                "All",
                icon = icon("check")
              )
            ),
            column(
              width = 1,
              align = "left",
              actionButton(
                "desel_all_mt",
                "None",
                icon = icon("xmark")
              )
            ),
            column(
              width = 10,
              align = "center",
              br(),
              uiOutput("multi_select_issues")
            )
          )
        )
        
        output$metadata_multi_box <- renderUI({
          column(
            width = 11,
            align = "left",
            hr(), br(),
            uiOutput("multi_select_issue_info"),
            br(), br(),
            actionButton(
              inputId = "conf_meta_multi",
              label = "Confirm",
              icon = icon("arrow-right")
            )
          )
        }) 
      } else {
        output$metadata_multi_box <- NULL
      }
    }
  })
  
  # Check if ongoing Multi Typing - Render accordingly
  observe({
    req(Typing$file_selection)
    
    # Folder selection
    shinyDirChoose(input,
                   "assembly_folder",
                   roots = c(Home = path_home(), Root = "/"),
                   defaultRoot = "Home",
                   session = session,
                   filetypes = c('', 'fasta', 'fna', 'fa'))
    
    Typing$assembly_folder_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$assembly_folder)
    
    # File(s) selection
    shinyFileChoose(input,
                    "assembly_files",
                    roots = c(Home = path_home(), Root = "/"),
                    defaultRoot = "Home",
                    session = session,
                    filetypes = c('', 'fasta', 'fna', 'fa'))
    
    Typing$assembly_files_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$assembly_files)
    
    # Format selection
    if(Typing$file_selection != "") {
      if((!is.null(Typing$assembly_files_path) | !is.null(Typing$assembly_folder_path)) & 
         !is.null(Typing$file_selection)) {
        if(Typing$file_selection == "files") {
          Typing$files_filtered <- Typing$assembly_files_path$name[which(!endsWith(Typing$assembly_files_path$name, ".gz") &
                                                                           grepl("\\.fasta|\\.fna|\\.fa", Typing$assembly_files_path$name))]
        } else if(Typing$file_selection == "folder") {
          files_selected <- list.files(as.character(Typing$assembly_folder_path))
          Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
                                                          grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
        } 
      }
    }
    
    multi_sel_table <- data.frame(
      Include = rep(TRUE, length(Typing$files_filtered)),
      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
                   Typing$files_filtered),
      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
                 "\\1", Typing$files_filtered, perl = F),
      Host = rep("", length(Typing$files_filtered)),
      Country = rep("", length(Typing$files_filtered)),
      City = rep("", length(Typing$files_filtered)),
      Isolation.Date = rep(format(Sys.Date()), length(Typing$files_filtered)))
    
    colnames(multi_sel_table)[7] <- "Isolation Date"
    
    Typing$multi_sel_table <- multi_sel_table
    
    if(nrow(Typing$multi_sel_table) > 0) {
      output$multi_select_tab_ctrls <- renderUI(
        fluidRow(
          h3(p("Metadata Declaration"), style = "color:white; margin-left: 15px"),
          br(),
          column(
            width = 1,
            align = "left",
            actionButton(
              "sel_all_mt",
              "All",
              icon = icon("check")
            )
          ),
          column(
            width = 1,
            align = "left",
            actionButton(
              "desel_all_mt",
              "None",
              icon = icon("xmark")
            )
          ),
          column(
            width = 10,
            align = "center",
            br(),
            uiOutput("multi_select_issues")
          )
        )
      )
    } else {
      output$multi_select_tab_ctrls <- NULL
    }
    
    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
      output$multi_select_table <- renderRHandsontable({
        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
                             stretchH = "all", contextMenu = FALSE
        ) %>%
          hot_cols(columnSorting = FALSE) %>%
          hot_rows(rowHeights = 25) %>%
          hot_col(2, readOnly = FALSE,
                  valign = "htBottom") %>%
          hot_col(3, readOnly = TRUE) %>%
          hot_col(1,
                  halign = "htCenter",
                  valign = "htTop", 
                  colWidths = 60) %>%
          hot_col(7, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                  validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }")
        
        htmlwidgets::onRender(rht, sprintf(
          "function(el, x) {
        var hot = this.hot;
        
        var columnData = hot.getDataAtCol(1); // Change column index if needed
        var duplicates = {};
          
        var highlightInvalidAndDuplicates = function(invalidValues) {
          
          var columnData = hot.getDataAtCol(1); // Change column index if needed
          var duplicates = {};

          // Find all duplicate values
          for (var i = 0; i < columnData.length; i++) {
            var value = columnData[i];
            if (value !== null && value !== undefined) {
              if (duplicates[value]) {
                duplicates[value].push(i);
              } else {
                duplicates[value] = [i];
              }
            }
          }

          // Reset all cell backgrounds in the column
          for (var i = 0; i < columnData.length; i++) {
            var cell = hot.getCell(i, 1); // Change column index if needed
            if (cell) {
              cell.style.background = 'white';
            }
          }

          // Highlight duplicates and invalid values
          for (var i = 0; i < columnData.length; i++) {
            var cell = hot.getCell(i, 1); // Change column index if needed
            var value = columnData[i];
            if (cell) {
              if (invalidValues.includes(value)) {
                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
              } else if (duplicates[value] && duplicates[value].length > 1) {
                cell.style.background = '#FF7334'; // Highlight color for duplicates
              }
            }
          }
        };

        var changefn = function(changes, source) {
          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
            highlightInvalidAndDuplicates(%s);
          }
        };

        hot.addHook('afterChange', changefn);
        hot.addHook('afterLoadData', function() {
          highlightInvalidAndDuplicates(%s);
        });
        hot.addHook('afterRender', function() {
          highlightInvalidAndDuplicates(%s);
        });

        highlightInvalidAndDuplicates(%s); // Initial highlight on load
        
        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
          var colData = hot.getDataAtCol(0);
          for (var i = 0; i < colData.length; i++) {
            hot.setDataAtCell(i, 0, message.value);
          }
          hot.render(); // Re-render the table
        });
      }", 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id())))
      })
      
    } else if(nrow(Typing$multi_sel_table) > 15) {
      output$multi_select_table <- renderRHandsontable({
        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
                             stretchH = "all", height = 500,
                             contextMenu = FALSE
        ) %>%
          hot_cols(columnSorting = FALSE) %>%
          hot_rows(rowHeights = 25) %>%
          hot_col(2,
                  readOnly = FALSE,
                  valign = "htBottom") %>%
          hot_col(3, readOnly = TRUE) %>%
          hot_col(1,
                  halign = "htCenter",
                  valign = "htTop", 
                  colWidths = 60) %>%
          hot_col(7, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
                  validator = "
                                function (value, callback) {
                                  var today_date = new Date();
                                  today_date.setHours(0, 0, 0, 0);
                                  
                                  var new_date = new Date(value);
                                  new_date.setHours(0, 0, 0, 0);
                                  
                                  try {
                                    if (new_date <= today_date) {
                                      callback(true);
                                      Shiny.setInputValue('invalid_date', false);
                                    } else {
                                      callback(false); 
                                      Shiny.setInputValue('invalid_date', true);
                                    }
                                  } catch (err) {
                                    console.log(err);
                                    callback(false); 
                                    Shiny.setInputValue('invalid_date', true);
                                  }
                                }")
        
        htmlwidgets::onRender(rht, sprintf(
          "function(el, x) {
        var hot = this.hot;
        
        var columnData = hot.getDataAtCol(1); // Change column index if needed
        var duplicates = {};
          
        var highlightInvalidAndDuplicates = function(invalidValues) {
          
          var columnData = hot.getDataAtCol(1); // Change column index if needed
          var duplicates = {};

          // Find all duplicate values
          for (var i = 0; i < columnData.length; i++) {
            var value = columnData[i];
            if (value !== null && value !== undefined) {
              if (duplicates[value]) {
                duplicates[value].push(i);
              } else {
                duplicates[value] = [i];
              }
            }
          }

          // Reset all cell backgrounds in the column
          for (var i = 0; i < columnData.length; i++) {
            var cell = hot.getCell(i, 1); // Change column index if needed
            if (cell) {
              cell.style.background = 'white';
            }
          }

          // Highlight duplicates and invalid values
          for (var i = 0; i < columnData.length; i++) {
            var cell = hot.getCell(i, 1); // Change column index if needed
            var value = columnData[i];
            if (cell) {
              if (invalidValues.includes(value)) {
                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
              } else if (duplicates[value] && duplicates[value].length > 1) {
                cell.style.background = '#FF7334'; // Highlight color for duplicates
              }
            }
          }
        };

        var changefn = function(changes, source) {
          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
            highlightInvalidAndDuplicates(%s);
          }
        };

        hot.addHook('afterChange', changefn);
        hot.addHook('afterLoadData', function() {
          highlightInvalidAndDuplicates(%s);
        });
        hot.addHook('afterRender', function() {
          highlightInvalidAndDuplicates(%s);
        });

        highlightInvalidAndDuplicates(%s); // Initial highlight on load
        
        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
          var colData = hot.getDataAtCol(0);
          for (var i = 0; i < colData.length; i++) {
            hot.setDataAtCell(i, 0, message.value);
          }
          hot.render(); // Re-render the table
        });
      }", 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id()), 
          jsonlite::toJSON(dupl_mult_id())))
        
      })
      
    } else {
      output$multi_select_table <- NULL
    } 
  })
  
  ### Typing Events ----
  
  # Confirm typing metadata
  observeEvent(input$conf_meta_multi, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    
    multi_select_table <- hot_to_r(input$multi_select_table)[which(hot_to_r(input$multi_select_table)$Include == TRUE), ]
    
    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
      show_toast(
        title = "Assembly ID(s) already present",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if (any(duplicated(multi_select_table$Files))) {
      show_toast(
        title = "Duplicated filename(s)",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if (any(multi_select_table$Files == "")) {
      show_toast(
        title = "Empty filename(s)",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
      show_toast(
        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if (!any(multi_select_table$Include == TRUE)) {
      show_toast(
        title = "No files selected",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
      show_toast(
        title = "Empty spaces in filename(s) not allowed",
        type = "error",
        position = "bottom-end",
        timer = 3000
      )
    } else if (isFALSE(Typing$reload)) {
      show_toast(
        title = "Reload Database first",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else if(Screening$status == "started") {
      show_toast(
        title = "Pending Single Typing",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      
      showModal(
        div(
          class = "typing-modal",
          modalDialog(
            column(
              width = 12,
              align = "left",
              br(),
              br(),
              HTML(
                paste(
                  '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
                  "<span style='color: white;'>",
                  "&nbsp",
                  nrow(multi_select_table),
                  " assemblies queried for Allelic Typing\n"
                )
              ),
              br(), br(),
              HTML(
                paste(
                  '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
                  "<span style='color: white;'>",
                  "&nbsp",
                  "Typing by <strong>",
                  DB$scheme,
                  "</strong> scheme."
                )
              ),
              br(), br(), br(),
              div(
                class = "save-assembly",
                materialSwitch(
                  "save_assembly_mt",
                  h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
                  value = TRUE,
                  right = TRUE)
              ),
              HTML(
                paste(
                  "<span style='color: orange;font-style:italic'>",
                  "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
                )
              ),
              br(), br(), br(), br(),
            ),
            title = "Start Allelic Typing",
            fade = TRUE,
            easyClose = TRUE,
            footer = tagList(
              modalButton("Cancel"),
              actionButton(
                "start_typ_multi",
                "Start",
                icon = icon("circle-play")
              )
            )
          )    
        )
      )
    }
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')
  })
  
  # Set reactive variable to distinguish files/folder selection
  observeEvent(input$assembly_files, {
    Typing$file_selection <- "files"
  })
  
  observeEvent(input$assembly_folder, {
    Typing$file_selection <- "folder"
  })
  
  observeEvent(input$sel_all_mt, {
    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
  })
  
  observeEvent(input$desel_all_mt, {
    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
  })
  
  # Print Log
  output$print_log <- downloadHandler(
    filename = function() {
      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
      paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
    },
    content = function(file) {
      writeLines(readLines(file.path(logdir, "script_log.txt")), file)
    }
  )
  
  # Reset Multi Typing
  observeEvent(input$reset_multi, {
    if(!grepl("Multi Typing", tail(readLines(file.path(logdir, "script_log.txt")), n = 1))) {
      showModal(
        div(
          class = "start-modal",
          modalDialog(
            fluidRow(
              br(), 
              column(
                width = 11,
                p(
                  HTML(
                    paste0(
                      '<span style="color: white; display: block; font-size: 15px; margin-left: 15px;">',
                      "A Multi Typing process is still pending. Stopping this process will cancel the processing.",
                      '</span>'
                    )
                  )
                )
              ),
              br()
            ),
            title = "Reset Multi Typing",
            fade = TRUE,
            easyClose = TRUE,
            footer = tagList(
              modalButton("Cancel"),
              actionButton("conf_multi_kill", "Stop", class = "btn btn-danger")
            )
          )
        )
      )
    } else {
      
      log_print("Reset multi typing")
      
      # Reset multi typing result list
      saveRDS(list(), file.path(app_local_share_path, "event_list.rds"))
      multi_help <- FALSE
      Typing$result_list <- NULL
      
      # Null logfile
      writeLines("0", file.path(logdir, "script_log.txt"))
      
      # Reset User Feedback variable
      Typing$multi_started <- FALSE
      
      output$initiate_multi_typing_ui <- initiate_multi_typing_ui
      
      output$pending_typing <- NULL
      output$multi_typing_results <- NULL
    }
  })
  
  # Confirm Reset after 
  observeEvent(input$conf_multi_kill, {
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "block";')
    removeModal()
    
    log_print("Kill multi typing")
    
    # Kill multi typing and reset logfile  
    system(paste("bash", paste0(getwd(), "/bin/kill_multi.sh")),  
           wait = TRUE)
    
    show_toast(
      title = "Execution cancelled",
      type = "warning",
      position = "bottom-end",
      timer = 6000
    )
    
    # Kill multi typing and reset logfile  
    writeLines("0", file.path(logdir, "script_log.txt"))
    
    #Reset multi typing result list
    saveRDS(list(), file.path(app_local_share_path, "event_list.rds"))
    multi_help <- FALSE
    Typing$result_list <- NULL
    
    # Reset User Feedback variable
    output$pending_typing <- NULL
    output$multi_typing_results <- NULL
    Typing$multi_started <- FALSE
    
    output$initiate_multi_typing_ui <- initiate_multi_typing_ui
    
    shinyjs::runjs('document.getElementById("blocking-overlay").style.display = "none";')  
  })
  
  observeEvent(input$start_typ_multi, {
    log_print("Initiate multi typing")
    
    if (Screening$status == "started") {
      show_toast(
        title = "Pending Gene Screening",
        type = "warning",
        position = "bottom-end",
        timer = 6000
      )
    } else {
      removeModal()
      
      show_toast(
        title = "Multi Typing started",
        type = "success",
        position = "bottom-end",
        timer = 10000
      )
      
      # Remove Allelic Typing Controls
      output$initiate_multi_typing_ui <- NULL
      output$metadata_multi_box <- NULL
      output$start_multi_typing_ui <- NULL
      
      # Activate entry detection
      DB$check_new_entries <- TRUE
      
      # Initiate Feedback variables
      Typing$multi_started <- TRUE
      Typing$pending <- TRUE
      
      # Arrange metadata
      multi_select_table <- hot_to_r(input$multi_select_table)
      
      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
      
      if(Typing$file_selection == "folder") {
        genome_folder <- as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$assembly_folder))
      } else if(Typing$file_selection == "files") {
        genome_folder <- dirname(Typing$assembly_files_path$datapath[1])
      }
      
      # Save metadata RDS file for bash script
      multi_typing_df <- list(
        db_path = Startup$database,
        wd = getwd(),
        metadata = hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,],
        save = input$save_assembly_mt,
        scheme = paste0(gsub(" ", "_", DB$scheme)),
        genome_folder = genome_folder,
        filenames = paste0(filenames, collapse= " "),
        genome_names = genome_names,
        alleles = file.path(Startup$database, gsub(" ", "_", DB$scheme), paste0(gsub(" ", "_", DB$scheme), "_alleles"))
      )
      
      saveRDS(multi_typing_df, file.path(app_local_share_path, "multi_typing_df.rds"))
      
      # Execute multi blat script  
      system(paste("bash", paste0(getwd(), "/bin/multi_typing.sh")), wait = FALSE)
    }
  })
  
  
  ### User Feedback ----
  
  observe({
    if(file.exists(file.path(logdir, "script_log.txt"))) {
      if(isTRUE(Typing$multi_started)) {
        check_multi_status()
      } else {
        Typing$status <- "Inactive"
      }
    }
  })
  
  check_multi_status <- reactive({
    
    invalidateLater(3000, session)
    
    log <- readLines(file.path(logdir, "script_log.txt"))
    
    # Check typing status
    if(str_detect(tail(log, 1), "Attaching")) {
      Typing$status <- "Attaching"
    } else if(str_detect(tail(log, 1), "Successful")) {
      Typing$multi_help <- TRUE
      Typing$status <- "Successful"
      show_toast(
        title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
        type = "success",
        position = "bottom-end",
        timer = 8000
      )
    } else if(str_detect(tail(log, 1), "failed")) {
      Typing$status <- "Failed"
      show_toast(
        title = sub(".* - ", "", tail(log, 1)),
        type = "error",
        position = "bottom-end",
        timer = 8000
      )
    } else if(str_detect(tail(log, 1), "Processing")) {
      Typing$status <- "Processing"
      
      if(any(str_detect(tail(log, 2), "Successful"))) {
        
        if(!identical(Typing$last_success, tail(log, 2)[1])) {
          Typing$multi_help <- TRUE
          show_toast(
            title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
            type = "success",
            position = "bottom-end",
            timer = 8000
          )
          
          Typing$last_success <- tail(log, 2)[1]
        }
      } else if(any(str_detect(tail(log, 2), "failed"))) {
        
        if(!identical(Typing$last_failure, tail(log, 2)[1])) {
          
          show_toast(
            title = sub(".* - ", "", tail(log, 2)[1]),
            type = "error",
            position = "bottom-end",
            timer = 8000
          )
          
          Typing$last_failure <- tail(log, 2)[1]
        }
      }
    } else if(str_detect(tail(log, 1), "finalized")) {
      Typing$multi_help <- TRUE
      Typing$status <- "Finalized"
      
      if(isTRUE(Typing$pending)) {
        show_toast(
          title = "Typing finalized",
          type = "success",
          position = "bottom-end",
          timer = 8000
        )
        
        Typing$pending <- FALSE
      }
    }
  })
  
  observe({
    if(!is.null(input$multi_results_picker)) {
      Typing$multi_table_length <- nrow(Typing$result_list[[input$multi_results_picker]])
    } else {
      Typing$multi_table_length <- NULL
    }
  })
  
  observe({
    if(!is.null(Typing$result_list)) {
      if(length(Typing$result_list) > 0) {
        if(is.null(Typing$multi_table_length)) {
          output$multi_typing_result_table <- renderDataTable(
              Typing$result_list[[input$multi_results_picker]],
              selection = "single",
              options = list(pageLength = 10,
                             columnDefs = list(list(searchable = TRUE,
                                                    targets = "_all")),
                             initComplete = DT::JS(
                               "function(settings, json) {",
                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             ),
                             drawCallback = DT::JS(
                               "function(settings) {",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             )
                            )
              )
        } else {
          if(Typing$multi_table_length > 15) {
            output$multi_typing_result_table <- renderDataTable(
              Typing$result_list[[input$multi_results_picker]],
              selection = "single",
              options = list(pageLength = 10,
                             columnDefs = list(list(searchable = TRUE,
                                                    targets = "_all")),
                             initComplete = DT::JS(
                               "function(settings, json) {",
                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             ),
                             drawCallback = DT::JS(
                               "function(settings) {",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             )))
          } else {
            output$multi_typing_result_table <- renderDataTable(
              Typing$result_list[[input$multi_results_picker]],
              selection = "single",
              options = list(pageLength = 10,
                             columnDefs = list(list(searchable = TRUE,
                                                    targets = "_all")),
                             initComplete = DT::JS(
                               "function(settings, json) {",
                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             ),
                             drawCallback = DT::JS(
                               "function(settings) {",
                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                               "}"
                             )))
          }
        }
      } else {
        output$multi_typing_result_table <- NULL
      }
    } else {
      output$multi_typing_result_table <- NULL
    }
  })
  
  observe({
    if(!is.null(Typing$multi_result_status)) {
      if(Typing$multi_result_status == "start" | Typing$multi_result_status == "finalized"){
        
        if(Typing$multi_help == TRUE) {
          Typing$result_list <- readRDS(file.path(app_local_share_path, "event_list.rds"))
          Typing$multi_help <- FALSE
        }
      } 
    }
  })
  
  #Render multi typing result feedback table
  observe({
    
    if(!is.null(Typing$result_list)) {
      if(length(Typing$result_list) > 0) {
        output$multi_typing_results <- renderUI({
          column(
            width = 12,
            fluidRow(
              column(1),
              column(
                width = 9,
                br(), br(),
                br(), br(),
                br(), 
                div(
                  class = "mult_res_sel",
                  selectInput(
                    "multi_results_picker",
                    label = h5("Select Typing Results", style = "color:white"),
                    choices = names(Typing$result_list),
                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
                  )
                ),
                br(), br()
              )
            ),
            dataTableOutput("multi_typing_result_table")
          )
        })
      }
    }
  })
  
  observe({
    
    # Render log content
    output$logText <- renderPrint({
      cat(rev(paste0(tail(readLogFile(), 50), "\n")))
    })
    
    output$logTextFull <- renderPrint({
      cat(rev(paste0(readLines(file.path(logdir, "script_log.txt")), "\n")))
    })
    
    # Render Pending UI
    if(!grepl("Multi Typing", tail(readLogFile(), n = 1)) & grepl("Start Multi Typing", head(readLogFile(), n = 1))) {
      
      Typing$multi_result_status <- "start"
      
      output$initiate_multi_typing_ui <- NULL
      
      output$pending_typing <- renderUI({
        fluidRow(
          fluidRow(
            br(), br(),
            column(width = 2),
            column(
              width = 4,
              h3(p("Pending Typing ..."), style = "color:white"),
              br(), br(),
              fluidRow(
                column(
                  width = 5,
                  HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:24px;color:white;margin-top:5px"></i>'))
                ),
                column(
                  width = 6,
                  align = "left",
                  actionButton(
                    "reset_multi",
                    "Terminate",
                    icon = icon("ban")
                  )
                )
              ),
            )
          ),
          br(), br(),
          fluidRow(
            column(width = 2),
            column(
              width = 10,
              verbatimTextOutput("logText")
            )  
          )
        )
      })
    } else if(grepl("Multi Typing finalized", tail(readLogFile(), n = 1))) {
      
      Typing$multi_result_status <- "finalized"
      
      Typing$last_scheme <- NULL
      
      output$initiate_multi_typing_ui <- NULL
      
      output$pending_typing <- renderUI({
        
        fluidRow(
          fluidRow(
            br(), br(),
            column(width = 2),
            column(
              width = 4,
              h3(p("Pending Multi Typing ..."), style = "color:white"),
              br(), br(),
              HTML(paste("<span style='color: white;'>", 
                         paste("Typing of", sum(str_detect(readLines(file.path(logdir, "script_log.txt")), "Processing")), "assemblies finalized."),
                         paste(sum(str_detect(readLines(file.path(logdir, "script_log.txt")), "Successful")), "successes."),
                         paste(sum(str_detect(readLines(file.path(logdir, "script_log.txt")), "failed")), "failures."),
                         "Reset to start another typing process.", 
                         sep = '<br/>')),
              br(), br(),
              fluidRow(
                column(
                  width = 5,
                  actionButton(
                    "reset_multi",
                    "Reset",
                    icon = icon("arrows-rotate")
                  )
                ),
                column(
                  width = 5,
                  downloadButton(
                    "print_log",
                    "Logfile",
                    icon = icon("floppy-disk")
                  )
                )
              )
            )
          ),
          br(), br(),
          fluidRow(
            column(width = 2),
            column(
              width = 10,
              verbatimTextOutput("logTextFull")
            )
          )
        )
      })
    } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
      output$pending_typing <- NULL
      Typing$multi_result_status <- "idle"
    }
  })
} # end server

# _______________________ ####

# Shiny ----

shinyApp(ui = ui, server = server)