Merge pull request #310 from lishensuo/develop24

add daily-gene module

R/tcga_surv.R

@@ -44,7 +44,7 @@ tcga_surv_get <- function(item,
     install.packages("stringr")
   }
 
-  print(head(TCGA_cli_data))
+  # print(head(TCGA_cli_data))
   # type 有几种额外的 Xena 做过聚合的结果
   # "COADREAD" "FPPP"     "GBMLGG"   "LUNG"     "PANCAN"
   # FPPP 好像不是正常的样本，不推荐使用，已去除

inst/shinyapp/modules/hom-daily-gene.R

@@ -0,0 +1,138 @@
+ui.home_daily_gene <- function(id) {
+  ns <- NS(id)
+  tagList(
+    # h3("Daily Gene", icon = "dice", align = "center"),
+    fluidRow(
+      column(6, #offset = 1,
+        uiOutput(ns("gene_tip")),
+
+        fluidRow(
+          column(12, align = "center",
+            actionBttn(
+               inputId = ns("change_gene"),
+               label = "Sample another one", 
+               style = "bordered",
+               color = "primary",
+               icon = icon("dice"),
+               size = "sm"
+            )
+          )
+        )
+      ),
+      column(6, #offset = 2,
+        uiOutput(ns("gene_cancer"))
+      )
+    ),
+    # fluidRow(
+    #   column(8, offset = 2,
+    #     uiOutput(ns("gene_cancer"))
+    #   )
+    # ),
+  )
+}
+
+
+
+
+
+server.home_daily_gene <- function(input, output, session) {
+  ns <- session$ns
+
+
+  gene_sp = reactiveValues(gene="TP53")
+
+
+  gene_sp = reactive({
+    if(input$change_gene==0){
+      current_date <- Sys.Date()
+      formatted_date <- as.integer(format(current_date, "%Y%m%d"))
+      set.seed(formatted_date)
+      gene_sp = sample(pancan_identifiers$gene,size = 1)
+    } else {
+      current_time <- Sys.time()
+      total_seconds <- as.integer(difftime(current_time, as.POSIXct("1970-01-01"), units = "secs"))
+      set.seed(total_seconds)
+      gene_sp = sample(pancan_identifiers$gene,size = 1)
+    } 
+    gene_sp
+  })
+
+  gene_data = reactive({
+    data.list = get_pancan_gene_value(gene_sp(), norm = "tpm")
+    data = data.list$expression
+    shiny::validate(
+      need(try(!all(is.na(data))), 
+        "Sorry, no valid value for the sampling gene. Pleaese click the button again."),
+    )   
+    data = data.frame(value=data) %>% 
+      tibble::rownames_to_column("sample") %>% 
+      dplyr::inner_join(tcga_gtex) %>% 
+      dplyr::mutate(tissue = as.character(tissue))
+    data
+  })
+
+
+
+  stat_res = reactive({
+    data = gene_data()
+    stat_res = compare_means(value ~ type2, data = data,  
+                             group.by = "tissue") %>% 
+      dplyr::arrange(p)
+    stat_res
+  })
+
+
+  output$gene_cancer = renderUI({
+    output$box_plot = renderPlotly({
+      data = gene_data()
+      p = data %>% 
+        dplyr::filter(tissue == stat_res()$tissue[1]) %>% 
+        dplyr::filter(value > -9.966) %>% 
+        ggboxplot(x = "type2", y = "value", 
+                  fill = "type2", 
+                  color = "black",
+                  width = 0.5,
+                  palette = "aaas") + 
+        xlab(paste0("TCGA-",stat_res()$tissue[1])) + 
+        ylab("TPM value (TCGA+GTEx)") +
+        ggtitle(gene_sp(),
+                subtitle = paste0("Wilcoxon, p=", 
+                                  formatC(stat_res()$p[1], format = "e", digits = 2))) +
+        theme(legend.position = "none",
+              text = element_text(size = 12),
+              plot.title = element_text(hjust = 0.5),
+              plot.subtitle = element_text(size = 12, hjust = 0.5))
+        subtitle_txt = paste0("Wilcoxon, p=", formatC(stat_res()$p[1], format = "e", digits = 2))
+        title_text = 
+      p = ggplotly(p) %>%
+        layout(title = list(text = paste0(gene_sp(),'<br>','<sup>', subtitle_txt,'</sup>'),
+                            font = list(size = 18)),
+               xaxis = list(font=list(size = 15)),
+               yaxis = list(font=list(size = 10)))
+      p
+    })
+    plotlyOutput(ns("box_plot"), height = "220px")
+  })
+
+
+  output$gene_tip = renderUI({
+
+    tcga_link = "https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations"
+    gc_link = paste0("https://www.genecards.org/cgi-bin/carddisp.pl?gene=", gene_sp())
+    pm_link = paste0("https://pubmed.ncbi.nlm.nih.gov/?term=%28",gene_sp(),"%29+AND+%28cancer%29")
+    tagList(
+      tags$ul(
+        tags$li(gene_sp()," is most differentially expressed in ",
+                a(paste0("TCGA-",stat_res()$tissue[1]), href = tcga_link), ".",
+                style = "font-size: 16px;"),
+        tags$li("Explore its pan-cancer feature in right panel. ☞",style = "font-size: 16px;"),
+        tags$li("Search more about the gene in ",
+                a("GeneCards", href = gc_link), " or ",
+                a("PubMed", href = pm_link), ".",
+                style = "font-size: 16px;")
+      )
+    )
+  })
+}
+
+

inst/shinyapp/modules/home-pancan-search.R

@@ -30,6 +30,7 @@ ui.home_search_box <- function(id) {
         )
       )
     ),
+    br(),
     fluidRow(
       column(11, offset = 1,
         h5(strong("2.Run two explorations:"))
@@ -214,7 +215,7 @@ server.home_search_box <- function(input, output, session) {
               br(),
               h3("NOTEs:"),
               h4("1. It will take about ",strong("one minute",style="color:red")," for the general analysis which includes the relationships between queried molecule and ",
-                "(1) chinical phenotypes, (2) survival influence, (3) tumor index (4) immune infiltration, (5) pathway activity.",
+                "(1) clinical phenotypes, (2) survival influence, (3) tumor index (4) immune infiltration, (5) pathway activity.",
                 "You can see the ",a("example report", href = "https://lishensuo.github.io/book_test/UCSCXenaShiny_example_report.html")," while waiting."),
               h4("2. It will take about ", strong("10 seconds",style="color:red"), " for the generation of organized report in html format."),
               h4("3. Final, the analyzed result under the report can be directly downloaded in zip format.")

inst/shinyapp/server/modules.R

@@ -183,4 +183,4 @@ observeEvent(req(input$navbar %in% c(
 
 
 callModule(server.home_search_box, "homepage_pancan_search")
-
+callModule(server.home_daily_gene, "homepage_daily_gene")

inst/shinyapp/ui/home.R

@@ -8,7 +8,7 @@ ui.page_home <- function() {
         tags$link(rel = "stylesheet", type = "text/css", href = "bootstrap4.css")
       ),
       fluidRow(
-        column(5,
+        column(4,
           tags$div(
             column(
               12,
@@ -34,29 +34,21 @@ ui.page_home <- function() {
             )
           )
         ),
+        column(4,
+          wellPanel(
+            style = "background: #b3cde3",
+            h3("❤ Daily Gene", icon = "dice", align = "center"),
+            ui.home_daily_gene("homepage_daily_gene"),
+          )
+        ),
         column(4,
           wellPanel(
             style = "background: #a6cee3",
-            h2("TCGA Pan-Cancer Query!", align = "center"),
+            h3("❤ Pan-Cancer Query", align = "center"),
             # br(),
             ui.home_search_box("homepage_pancan_search"),
           )
         ),
-        column(3,
-          wellPanel(
-            style = "background: #b3cde3",
-            h2("Latest Release Notes", align = "center"),
-            br(),
-            tags$ul(
-              tags$li("2024-01-21: Adjust homepge with slick gallery to show basic page help.",style = "font-size: 14px;"),
-              tags$li("2024-01-16: Introduce MSigDB genesets  for molecule batch analysis.",style = "font-size: 14px;"),
-              tags$li("2023-12-20: Add  download modules that support data requisition.",style = "font-size: 14px;"),
-              tags$li("See more update logs in", 
-                a("Github", href="https://github.com/openbiox/UCSCXenaShiny"),
-                style = "font-size: 16px;")
-            )
-          )
-        )
       ),
       tags$br(),
       h2(strong("※ Shiny Page Gallery")),
@@ -68,7 +60,7 @@ ui.page_home <- function() {
         )
       ),
       br(),br(),
-      h2(strong("※ Quick TCGA modules with specific functions")),
+      h2(strong("※ Custom TCGA modules with specific functions")),
       tags$hr(style = "border:none; border-top:5px solid #5E81AC;"),
       fluidRow(
         column(
@@ -240,8 +232,28 @@ ui.page_home <- function() {
               "similar versatile pipeline analyses (including comparison, correlation, survival) with  personalized operations for PCAWG and CCLE databases."))
           )
         )
+      ),
+      br(),
+      h2(strong("※ Latest significant release notes")),
+      tags$hr(style = "border:none; border-top:5px solid #5E81AC;"),
+      fluidRow(
+        column(12, #offset = 1,
+          tags$ul(
+            tags$li("2024-02-14: Incorporate the PharmacoGenomics analysis modules",style = "font-size: 20px;"),
+            tags$li("2024-01-21: Adjust homepge with slick gallery to show basic page help.",style = "font-size: 20px;"),
+            tags$li("2024-01-16: Introduce MSigDB genesets for molecule batch analysis.",style = "font-size: 20px;"),
+            tags$li("2023-12-20: Add download modules that support data requisition.",style = "font-size: 20px;"),
+            tags$li("See more update logs in our", 
+              a("Github", href="https://github.com/openbiox/UCSCXenaShiny"), ".",
+              "If you have any questions, please report the ",
+              a("issue", href = "https://github.com/openbiox/UCSCXenaShiny/issues"),
+              " or email at [email protected]. We will get back to you ASAP.",
+              style = "font-size: 20px;")
+          )  
+        )
       )
     )
   )
 }
 
+

inst/shinyapp/ui/pancan-analysis-quick.R

@@ -1,6 +1,6 @@
 ui.page_pancan_quick <- function() {
   navbarMenu(
-    title = "Quick T·P·C Analysis",
+    title = "Custom T·P·C Modules",
     icon = icon("buromobelexperte"),
     # tabPanel(
     #   "Combo: Single Gene Analysis",

inst/shinyapp/ui/pancan-analysis-tcga.R

@@ -1,6 +1,6 @@
 ui.page_pancan_tcga <- function() {
   navbarMenu(
-    title = "Personalized T·P·C Analysis",
+    title = "Personalized T·P·C Pipelines",
     icon = icon("buromobelexperte"),
     #### TCGA
     tabPanel(