Crash fix sig ana (#420)

* check for number of genes and trow explicit error * add hiding of tabs to avoid usage of results; ; fixes #417 * changed to show debug text again; to let user know what is going on addresses #421 (#423)
ICB-DCM · Dec 17, 2024 · 7ad0b54 · 7ad0b54
1 parent 9038884
commit 7ad0b54
Showing 1 changed file with 35 additions and 3 deletions.
diff --git a/program/shinyApp/server.R b/program/shinyApp/server.R
@@ -1434,11 +1434,15 @@ server <- function(input,output,session){
     # new object Created for res_tmp[[session$token]]
     res_tmp[[session$token]]$data <<- res_tmp[[session$token]]$data[rownames(res_tmp[[session$token]]$data),]
     par_tmp[[session$token]]['BatchColumn'] <<- input$BatchEffect_Column
-
     # preprocessing
     print(paste0("Do chosen Preprocessing:",input$PreProcessing_Procedure))
+
+    # Check for DESeq option if more than 100 genes avail as it is for omics!
+
     tryCatch({
-      if(input$PreProcessing_Procedure == "vst_DESeq"){
+      if(input$PreProcessing_Procedure == "vst_DESeq" & nrow(res_tmp[[session$token]]$data) < 100){
+        stop("DESeq Preprocessing is only recommended for omics (here for data with more than 100 genes). Change Pre-processing or your data input!")
+      }else if(input$PreProcessing_Procedure == "vst_DESeq"& nrow(res_tmp[[session$token]]$data) >= 100){
         res_tmp[[session$token]]$data <<- deseq_processing(
             data = res_tmp[[session$token]]$data,
             omic_type = par_tmp[[session$token]]$omic_type,
@@ -1455,6 +1459,16 @@ server <- function(input,output,session){
       }
     }, error = function(e){
       error_modal(e)
+      output$Statisitcs_Data <- renderText({
+        HTML("<span style='color: red;'>There has been an error</span><br>The current data might not be what you expect.<br>Ensure you change something within the data or the Pre-Processing,<br>and click 'Get Pre-Processing' again.<br><span style='color: red;'>You should not see this message before moving to analysis!</span><br>")
+      })
+      hideTab(inputId = "tabsetPanel1", target = "Sample Correlation")
+      hideTab(inputId = "tabsetPanel1", target = "Significance Analysis")
+      hideTab(inputId = "tabsetPanel1", target = "PCA")
+      hideTab(inputId = "tabsetPanel1", target = "Heatmap")
+      hideTab(inputId = "tabsetPanel1", target = "Single Gene Visualisations")
+      hideTab(inputId = "tabsetPanel1", target = "Enrichment Analysis")
+
       waiter$hide()
       req(FALSE)
     })
@@ -1469,9 +1483,18 @@ server <- function(input,output,session){
         )
       }, error = function(e){
         error_modal(
-          e, additional_text = "Batch correction failed. Make sure the batch effect column is correct!"
+          e, additional_text = "Batch correction failed. Make sure the batch effect column is correct or NULL!"
         )
         waiter$hide()
+        output$Statisitcs_Data <- renderText({
+          HTML("<span style='color: red;'>There has been an error</span><br>The current data might not be what you expect.<br>Ensure you change something within the data or the Pre-Processing,<br>and click 'Get Pre-Processing' again.<br><span style='color: red;'>You should not see this message before moving to analysis!</span><br>")
+        })
+        hideTab(inputId = "tabsetPanel1", target = "Sample Correlation")
+        hideTab(inputId = "tabsetPanel1", target = "Significance Analysis")
+        hideTab(inputId = "tabsetPanel1", target = "PCA")
+        hideTab(inputId = "tabsetPanel1", target = "Heatmap")
+        hideTab(inputId = "tabsetPanel1", target = "Single Gene Visualisations")
+        hideTab(inputId = "tabsetPanel1", target = "Enrichment Analysis")
         req(FALSE)
       })
     } else if (input$BatchEffect_Column != "NULL" & input$PreProcessing_Procedure == "vst_DESeq"){
@@ -1493,6 +1516,15 @@ server <- function(input,output,session){
           )
         )
         waiter$hide()
+        output$Statisitcs_Data <- renderText({
+          HTML("<span style='color: red;'>There has been an error</span><br>The current data might not be what you expect.<br>Ensure you change something within the data or the Pre-Processing,<br>and click 'Get Pre-Processing' again.<br><span style='color: red;'>You should not see this message before moving to analysis!</span><br>")
+        })
+        hideTab(inputId = "tabsetPanel1", target = "Sample Correlation")
+        hideTab(inputId = "tabsetPanel1", target = "Significance Analysis")
+        hideTab(inputId = "tabsetPanel1", target = "PCA")
+        hideTab(inputId = "tabsetPanel1", target = "Heatmap")
+        hideTab(inputId = "tabsetPanel1", target = "Single Gene Visualisations")
+        hideTab(inputId = "tabsetPanel1", target = "Enrichment Analysis")
         req(FALSE)
       })
     } else {