Error Handling enrichment Analysis (#164)

* Correct tryCatch placement, shiny does not fail anymore when supplying wrong organism or type of annotation. * Switching between Modals now, no double appearance. * Small adjustment to modal. * Added Contactmail
ICB-DCM · Jan 29, 2024 · 72ea5bd · 72ea5bd
1 parent ff79bc1
commit 72ea5bd
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Showing 2 changed files with 59 additions and 37 deletions.
diff --git a/program/shinyApp/R/enrichment_analysis/server.R b/program/shinyApp/R/enrichment_analysis/server.R
@@ -725,11 +725,16 @@ enrichment_analysis_Server <- function(id, data, params, updates){
         anno_results <- check_annotation_enrichment_analysis(ea_reactives$data)
         ea_reactives$data <- anno_results$new_data
         ea_reactives$can_start <- anno_results$can_start
-        if(anno_results$no_ann){
+        translation_modal <- function(){
           showModal(modalDialog(
             title = "No annotation type detected",
             footer = NULL,
-            p("No valid annotation type was detected in your row annotation. Please indicate the type of annotation with which you uploaded your genes."),
+            p(paste0(
+              "No valid annotation type was detected in your row annotation. ",
+              "Please indicate the type of annotation with which you uploaded your genes.\n",
+              "Here are the first 5 rownames of your row annotation: \n",
+              toString(rownames(ea_reactives$data)[1:5])
+            )),
             selectInput(
               inputId = ns("AnnotationSelection"),
               label = "Which annotation are you using?",
@@ -739,6 +744,9 @@ enrichment_analysis_Server <- function(id, data, params, updates){
             ),
             actionButton(inputId = ns("AMC"), label = "Proceed"),
           ))
+        }
+        if(anno_results$no_ann){
+          translation_modal()
         }else if(anno_results$can_start == FALSE){
           if(input$ORA_or_GSE == "GeneSetEnrichment"){
             ea_reactives$data <- translate_genes_ea(
@@ -757,25 +765,54 @@ enrichment_analysis_Server <- function(id, data, params, updates){
           }
           ea_reactives$can_start <- TRUE
         }
+        # Modal in case translation fails
+        observeEvent(input$translation_again, {
+          # close modal
+          removeModal()
+          # call translation again
+          translation_modal()
+        })
         # close modal on button click
         observeEvent(input$AMC, {
           anno_results$base_annotation <- input$AnnotationSelection
           removeModal()
-          if(input$ORA_or_GSE == "GeneSetEnrichment"){
-            ea_reactives$data <- translate_genes_ea(
-              data = ea_reactives$data,
-              annotation_results = anno_results,
-              input = input
-            )
-          }else{
-            ea_reactives$tmp_genes <<- translate_genes_oa(
-              annotation_results = anno_results,
-              input = input,
-              geneSetChoice = ea_reactives$tmp_genes,
-              geneSet2Enrich = input$GeneSet2Enrich
+          tryCatch(
+            {
+              if(input$ORA_or_GSE == "GeneSetEnrichment"){
+                ea_reactives$data <- translate_genes_ea(
+                  data = ea_reactives$data,
+                  annotation_results = anno_results,
+                  input = input
+                )
+              }else{
+                ea_reactives$tmp_genes <- translate_genes_oa(
+                  annotation_results = anno_results,
+                  input = input,
+                  geneSetChoice = ea_reactives$tmp_genes,
+                  geneSet2Enrich = input$GeneSet2Enrich
+                )
+              }
+              ea_reactives$can_start <- TRUE
+            },
+            error=function(e){
+              showModal(modalDialog(
+                title = HTML("<font color='red'>An Error occured</font>"),
+                footer = actionButton(
+                  inputId = ns("translation_again"),
+                  label = "Choose another annotation type"
+                ),
+                HTML(paste0(
+                  "<font color='red'>Error: ",e$message,"</font><br><br>",
+                  "It is highly likely that the error is caused by the fact that the ",
+                  "gene names in your data set do not match the gene names in the ",
+                  "annotation you selected. Please check your data set and annotation ",
+                  "and try again.<br><br>",
+                  "Otherwise, please contact the cOmicsArtist Lea and Paul ",
+                  "(<a href = 'mailto: [email protected]'>[email protected]</a>)."
+                ))
+              ))
+            }
             )
-          }
-          ea_reactives$can_start <- TRUE
         })
         # start the analysis if ea_reactives$can_start == TRUE
         observeEvent(ea_reactives$can_start, {

diff --git a/program/shinyApp/R/enrichment_analysis/translation.R b/program/shinyApp/R/enrichment_analysis/translation.R
@@ -9,28 +9,13 @@ translate_genes_ea <- function(data, annotation_results, input){
   }else{
     orgDb <- org.Mm.eg.db::org.Mm.eg.db
   }
-  tryCatch(
-    {
-      rowData(data)[["ENTREZID"]] <- AnnotationDbi::mapIds(
-        orgDb,
-        keys = rowData(data)[[annotation_results$base_annotation]],
-        column = "ENTREZID",
-        keytype = annotation_results$base_annotation
-      )
-      return(data)
-    },
-    error = function(e) {
-      show_toast(
-        title = "You chose the wrong Organism. Please restart the app.",
-        type = "info",
-        position = "top",
-        timerProgressBar = TRUE,
-        width = "30%"
-      )
-      # let the program wait for 5 seconds
-      Sys.sleep(3)
-    }
+  rowData(data)[["ENTREZID"]] <- AnnotationDbi::mapIds(
+    orgDb,
+    keys = rowData(data)[[annotation_results$base_annotation]],
+    column = "ENTREZID",
+    keytype = annotation_results$base_annotation
   )
+  return(data)
 }
 
 # input$GeneSet2Enrich