Merge pull request #305 from lishensuo/develop21

fig a bug when grouping sample
openbiox · Jan 27, 2024 · 2611fdd · 2611fdd
2 parents 515ade0 + 62b19ce
commit 2611fdd
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Showing 4 changed files with 18 additions and 10 deletions.
diff --git a/inst/shinyapp/modules/function/modules-z-group-sample.R b/inst/shinyapp/modules/function/modules-z-group-sample.R
@@ -281,17 +281,22 @@ group_samples_Server = function(input, output, session, database = "toil",
           dplyr::filter(Sample %in% samples())
       }
     }
-    x_data$level1 = L1_x
-    x_data$cancer = clinical_phe[,2,drop=T][match(x_data$Sample, clinical_phe$Sample)]
-    x_data = x_data[,c("id","level1","level2","Sample","value","cancer")] %>%
-      dplyr::arrange(cancer, Sample)
-    x_data
+    # req(nrow(x_data)>0)
+    if(nrow(x_data)>0){
+      x_data$level1 = L1_x
+      x_data$cancer = clinical_phe[,2,drop=T][match(x_data$Sample, clinical_phe$Sample)]
+      x_data = x_data[,c("id","level1","level2","Sample","value","cancer")] %>%
+        dplyr::arrange(cancer, Sample)
+      x_data
+    } else {
+      NULL
+    }
+
   })
   # output$condi_dist = renderPrint({head(condi_data())})
 
   output$condi_dist = renderPrint({
-    if(is.null(condi_data())) return("No item is chosen.")
-
+    if(is.null(condi_data())) return("No valid sammple for the identifier.")
     if(class(condi_data()[,"value",drop=TRUE])=="numeric"){
       summary(condi_data()[,"value",drop=TRUE])
     } else {
@@ -301,6 +306,7 @@ group_samples_Server = function(input, output, session, database = "toil",
 
 
   output$set_quantile.ui = renderUI({
+    req(!is.null(condi_data()))
     choice_chrs = condi_data()$value
     if(class(choice_chrs)!="character"){
       materialSwitch(ns("set_quantile"),"Whether group by percentile?",value = TRUE)
@@ -311,6 +317,7 @@ group_samples_Server = function(input, output, session, database = "toil",
   # 创建两分组
 
   output$set_group1.ui = renderUI({
+    req(!is.null(condi_data()))
     choice_chrs = condi_data()$value
     fluidRow(
       if(class(choice_chrs)=="character"){
@@ -339,6 +346,7 @@ group_samples_Server = function(input, output, session, database = "toil",
   })
 
   output$set_group2.ui = renderUI({
+    req(!is.null(condi_data()))
     choice_chrs = condi_data()$value
     fluidRow(
       if(class(choice_chrs)=="character"){

diff --git a/inst/shinyapp/server/modules.R b/inst/shinyapp/server/modules.R
@@ -144,7 +144,7 @@ observeEvent(req(input$navbar=="CCLE: Comparison Analysis"),{
 
 
 # # identifier help
-observeEvent(req(input$navbar=="Id reference"),{
+observeEvent(req(input$navbar=="ID Query"),{
 	callModule(server.modules_id_reference, "modules_id_reference")
 }, once = TRUE) 
 

diff --git a/inst/shinyapp/ui/pancan-analysis-quick.R b/inst/shinyapp/ui/pancan-analysis-quick.R
@@ -1,6 +1,6 @@
 ui.page_pancan_quick <- function() {
   navbarMenu(
-    title = "Quick TCGA/PCAWG/CCLE Analysis",
+    title = "Quick T·P·C Analysis",
     icon = icon("buromobelexperte"),
     # tabPanel(
     #   "Combo: Single Gene Analysis",

diff --git a/inst/shinyapp/ui/pancan-analysis-tcga.R b/inst/shinyapp/ui/pancan-analysis-tcga.R
@@ -1,6 +1,6 @@
 ui.page_pancan_tcga <- function() {
   navbarMenu(
-    title = "Personalized TCGA/PCAWG/CCLE Analysis",
+    title = "Personalized T·P·C Analysis",
     icon = icon("buromobelexperte"),
     #### TCGA
     tabPanel(