Merge pull request #311 from lishensuo/develop25

fix general analysis bugs
openbiox · Feb 26, 2024 · 8cccd3f · 8cccd3f
2 parents 7cea773 + 68ef912
commit 8cccd3f
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Showing 9 changed files with 78 additions and 57 deletions.
diff --git a/inst/shinyapp/modules/modules-z-download-1-pancan.R b/inst/shinyapp/modules/modules-z-download-1-pancan.R
@@ -169,7 +169,7 @@ ui.modules_download_pancan = function(id){
 							br(),br(),br(),br(),
 							dataTableOutput(ns("L3s_x_data")),
 							br(),
-							h3("3. Download results"),
+							h3("4. Download results"),
 						    fluidRow(
 						    	column(3, downloadButton(ns("save_csv"), "Download table(.csv)")),
 						    	column(3, offset = 2, downloadButton(ns("save_rda"), "Download table(.rda)"))

diff --git a/inst/shinyapp/modules/quick/modules-pancan-1-search.R b/inst/shinyapp/modules/quick/modules-pancan-1-search.R
@@ -138,6 +138,10 @@ server.modules_pancan_dist <- function(input, output, session) {
       selected = profile_choices()$default
     )
   })
+
+  observeEvent(input$Mode, {
+    updateTabsetPanel(inputId = "Mode_params", selected = input$Mode)
+  })
 
   opt_pancan = callModule(mol_origin_Server, "mol_origin2quick", database = "toil")
 

diff --git a/inst/shinyapp/modules/quick/modules-pancan-10-mut.R b/inst/shinyapp/modules/quick/modules-pancan-10-mut.R
@@ -11,7 +11,16 @@ ui.modules_pancan_mut = function(id){
 	              ns = ns,
 	              condition = "input.toggleBtn % 2 == 1",
 	              mol_origin_UI(ns("mol_origin2quick"), database = "toil")
-	            ),
+	            ), br(),
+	            virtualSelectInput(
+	              inputId = ns("mut_Gene"),
+	              label = "Grouping by gene mutation",
+	              choices = NULL,
+	              width = "100%",
+	              search = TRUE,
+	              allowNewOption = TRUE,
+	              dropboxWidth = "200%"
+	            ), br(),
 	            shinyWidgets::prettyRadioButtons(
 	              inputId = ns("profile"), label = "Select affected genomic profile:",
 	              choiceValues = c("mRNA", "transcript", "methylation", "miRNA"),
@@ -27,15 +36,6 @@ ui.modules_pancan_mut = function(id){
 	              allowNewOption = TRUE,
 	              dropboxWidth = "200%"
 	        	),
-	            virtualSelectInput(
-	              inputId = ns("mut_Gene"),
-	              label = "Grouping by gene mutation",
-	              choices = NULL,
-	              width = "100%",
-	              search = TRUE,
-	              allowNewOption = TRUE,
-	              dropboxWidth = "200%"
-	            ),
 	            shinyWidgets::prettyRadioButtons(
 	              inputId = ns("Mode"), label = "Select analysis cancer(s):",
 	              choiceValues = c("Pan-cancer", "Single-cancer"),

diff --git a/inst/shinyapp/modules/quick/modules-pancan-5-unicox.R b/inst/shinyapp/modules/quick/modules-pancan-5-unicox.R
@@ -29,6 +29,9 @@ ui.modules_pancan_unicox <- function(id) {
             dropboxWidth = "200%"
           ),
         ),
+      ),
+      column(
+        3,
         wellPanel(
           h4("2. Parameters", align = "center"),
           selectInput(inputId = ns("measure"), label = "Select Measure for plot", choices = c("OS", "PFI", "DSS", "DFI"), selected = "OS"),
@@ -68,14 +71,16 @@ ui.modules_pancan_unicox <- function(id) {
             color = "primary",
             block = TRUE,
             size = "sm"
-          ))
+          )
+        )
       ),
-      column(9,
+      column(6,
              fluidRow(
-              column(6, offset = 3,
+              column(8, offset = 2,
                plotOutput(ns("unicox_gene_tree"), height = "600px")
               )
              ),
+             # plotOutput(ns("unicox_gene_tree"), height = "600px"),
              hr(),
              h5("NOTEs:"),
              p("1. We define gene in certain cancer type as risky (log(Hazard Ratio) > 0) or protective (log(Hazard Ratio) < 0) or NS (No statistical significance, P value > 0.05)"),

diff --git a/inst/shinyapp/modules/quick/modules-pancan-9-pw-cor.R b/inst/shinyapp/modules/quick/modules-pancan-9-pw-cor.R
@@ -38,6 +38,9 @@ ui.modules_pw_cor = function(id){
 		          		dropboxWidth = "200%"
 		          	),
 		        ),
+			),
+			column(
+				3,
 		        wellPanel(
           			h4("2. Parameters", align = "center"),
 			        selectInput(inputId = ns("use_all"), label = "Use All Cancer Types", choices = c("TRUE", "FALSE"), selected = "FALSE"),
@@ -99,15 +102,15 @@ ui.modules_pw_cor = function(id){
 			          block = TRUE,
 			          size = "sm"
 			        )
-			    )
-
+			    )	
 			),
 			column(
-			    9,
-			    fluidRow(
-			    	column(6, offset = 3,
-			    		plotOutput(ns("pw_plot"), height = "600px",width = "600px"))
-			    ),
+			    6,
+			    # fluidRow(
+			    # 	column(6, offset = 3,
+			    # 		plotOutput(ns("pw_plot"), height = "600px",width = "600px"))
+			    # ),
+			    plotOutput(ns("pw_plot"), height = "600px"),
 			    hr(),
 			    h5("NOTEs:"),
 			    p("1. 500 common pathway genesets from 3 resources(50 HALLMARK, 186 KEGG, 264 IOBR) were collected."),

diff --git a/inst/shinyapp/modules/quick/modules-pcawg-1-search.R b/inst/shinyapp/modules/quick/modules-pcawg-1-search.R
@@ -41,6 +41,9 @@ ui.modules_pcawg_dist <- function(id) {
             placement = "right", options = list(container = "body")
           ),
         ),
+      ),
+      column(
+        3,
         wellPanel(
           h4("2. Parameters", align = "center"),
           materialSwitch(ns("pdist_mode"), "Show violin plot", inline = FALSE),
@@ -82,10 +85,10 @@ ui.modules_pcawg_dist <- function(id) {
             block = TRUE,
             size = "sm"
           )
-        )
+        ),
       ),
       column(
-        9,
+        6,
         plotOutput(ns("gene_pancan_dist"), height = "500px"),
         hr(),
         h5("NOTEs:"),

diff --git a/inst/shinyapp/modules/quick/modules-pcawg-2-unicox.R b/inst/shinyapp/modules/quick/modules-pcawg-2-unicox.R
@@ -36,6 +36,9 @@ ui.modules_pcawg_unicox <- function(id) {
             dropboxWidth = "200%"
           ),
         ),
+      ),
+      column(
+        3,
         wellPanel(
           h4("2. Parameters", align = "center"),
           # selectInput(inputId = ns("measure"), label = "Select Measure for plot", choices = c("OS", "PFI", "DSS", "DFI"), selected = "OS"),
@@ -52,35 +55,36 @@ ui.modules_pcawg_unicox <- function(id) {
             color = "primary",
             block = TRUE,
             size = "sm"
-          )),
-          wellPanel(
-            h4("3. Download", align = "center"),
-            numericInput(inputId = ns("height"), label = "Height", value = 8),
-            numericInput(inputId = ns("width"), label = "Width", value = 6),
-            prettyRadioButtons(
-              inputId = ns("device"),
-              label = "Choose plot format",
-              choices = c("pdf", "png"),
-              selected = "pdf",
-              inline = TRUE,
-              icon = icon("check"),
-              animation = "jelly",
-              fill = TRUE
-            ),
-            tags$hr(style = "border:none; border-top:2px solid #5E81AC;"),
-            downloadBttn(
-              outputId = ns("download"),
-              style = "gradient",
-              color = "primary",
-              block = TRUE,
-              size = "sm"
-            )
           )
         ),
+        wellPanel(
+          h4("3. Download", align = "center"),
+          numericInput(inputId = ns("height"), label = "Height", value = 8),
+          numericInput(inputId = ns("width"), label = "Width", value = 6),
+          prettyRadioButtons(
+            inputId = ns("device"),
+            label = "Choose plot format",
+            choices = c("pdf", "png"),
+            selected = "pdf",
+            inline = TRUE,
+            icon = icon("check"),
+            animation = "jelly",
+            fill = TRUE
+          ),
+          tags$hr(style = "border:none; border-top:2px solid #5E81AC;"),
+          downloadBttn(
+            outputId = ns("download"),
+            style = "gradient",
+            color = "primary",
+            block = TRUE,
+            size = "sm"
+          )
+        )
+      ),
       column(
-        9,
+        6,
         fluidRow(
-         column(6, offset = 3,
+         column(8, offset = 2,
           plotOutput(ns("unicox_gene_tree"), height = "600px")
          )
         ),

diff --git a/inst/shinyapp/server/repository.R b/inst/shinyapp/server/repository.R
@@ -394,7 +394,7 @@ observeEvent(input$show_R_code, {
 
 # ref: https://stackoverflow.com/questions/38706965/is-there-any-way-for-an-actionbutton-to-navigate-to-another-tab-within-a-r-shi
 observeEvent(input$analyze_data, {
-  updateNavbarPage(session = session, inputId = "navbar", selected = "General Analysis")
+  updateNavbarPage(session = session, inputId = "navbar", selected = "General Dataset Analysis")
 })
 
 # Show alert info when select rows from table -----------------------------

diff --git a/inst/shinyapp/ui/pancan-analysis-quick.R b/inst/shinyapp/ui/pancan-analysis-quick.R
@@ -42,18 +42,19 @@ ui.page_pancan_quick <- function() {
         "TCGA: Association Between Molecular Profile and Gene Mutation",
         ui.modules_pancan_mut("modules_pancan_mut")
     ),
-    tabPanel(
-      "TCGA: Molecular Profile Cox Analysis",
-      ui.modules_pancan_unicox("modules_pancan_unicox")
-    ),
     tabPanel(
       "TCGA: Molecular Profile Log-rank Analysis",
       ui.modules_sur_plot("modules_sur_plot")
     ),
+    tabPanel(
+      "TCGA: Molecular Profile Cox Analysis",
+      ui.modules_pancan_unicox("modules_pancan_unicox")
+    ),
     tabPanel(
         "TCGA: Dimension Reduction Distribution",
         ui.modules_dim_dist("modules_dim_dist")
     ),
+
     tabPanel(
       "PCAWG: Molecular Profile Distribution Across Cancer Types (Tumor VS Normal)",
       ui.modules_pcawg_dist("modules_pcawg_dist")
@@ -62,14 +63,15 @@ ui.page_pancan_quick <- function() {
       "PCAWG: Molecule-Molecule Correlation",
       ui.modules_pcawg_gene_cor("modules_pcawg_gene_cor")
     ),
-    tabPanel(
-      "PCAWG: Molecular Profile Cox Analysis",
-      ui.modules_pcawg_unicox("modules_pcawg_unicox")
-    ),
     tabPanel(
       "PCAWG: Molecular Profile Log-rank Analysis",
       ui.modules_pcawg_sur_plot("modules_pcawg_sur_plot")
     ),
+    tabPanel(
+      "PCAWG: Molecular Profile Cox Analysis",
+      ui.modules_pcawg_unicox("modules_pcawg_unicox")
+    ),
+
     tabPanel(
       "CCLE: Molecular Profile Distribution Across Cancer Primary Sites",
       ui.modules_ccle_dist("modules_ccle_dist")