Report of EA only created once and not automatically when doing anoth…

…er EA (#295) * Report of EA only created once and not automatically when doing another EA * small bugs
ICB-DCM · Aug 9, 2024 · da8ee67 · da8ee67
1 parent 1e0b8e7
commit da8ee67
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Showing 2 changed files with 17 additions and 5 deletions.
diff --git a/program/shinyApp/R/enrichment_analysis/server.R b/program/shinyApp/R/enrichment_analysis/server.R
@@ -119,7 +119,10 @@ enrichment_analysis_geneset_server <- function(
           )}
         )
         # download section
-        observeEvent(input$only2Report,{
+        session$userData[[paste0(id, "_Report")]] <- observeEvent(input$only2Report,{
+          if(!is.null(session$userData[[paste0(id, "_Report_Val")]])){
+            req(input$only2Report > session$userData[[paste0(id, "_Report_Val")]])
+          }
           notificationID <- showNotification(ui = "Saving...",duration = 0)
           tmp_filename <- paste0(getwd(),file_path, paste(id,Sys.time(),".png",sep="_"))
           ggsave(
@@ -175,7 +178,14 @@ enrichment_analysis_geneset_server_reactive <- function(
 ){
   observe({
     result <- result_all()[[paste("EnrichmentRes", id, sep = "_")]]
-    enrichment_analysis_geneset_server(id, result, organism_choice, gene_set_choice, ea_type)
+    # remove old observers and change base value
+    if (!is.null(session$userData[[paste0(id, "_Report")]])) {
+      session$userData[[paste0(id, "_Report_Val")]] <- isolate(
+        input[[paste0("EnrichmentAnalysis-", id, "-only2Report")]]
+      )
+      session$userData[[paste0(id, "_Report")]]$destroy()
+    }
+    server <- enrichment_analysis_geneset_server(id, result, organism_choice, gene_set_choice, ea_type)
   })
 }
 
@@ -202,10 +212,12 @@ enrichment_analysis_Server <- function(id, data, params, updates){
         'MIR_Legacy', 'GTRD', 'TFT_Legacy', 'CGN', 'CM', 'GO_BP', 'GO_CC', 'GO_MF',
         'HPO', 'IMMUNESIGDB', 'VAX'
       )
+
+      # Delete and Re-create the servers
       lapply(gene_sets_to_compare, function(id) {
         enrichment_analysis_geneset_server_reactive(
           id = id,
-          result = reactive(ea_reactives$enrichment_results),
+          result_all = reactive(ea_reactives$enrichment_results),
           ea_type = input$ORA_or_GSE,
           organism_choice = ea_reactives$organism,
           gene_set_choice = ea_reactives$tmp_genes

diff --git a/program/shinyApp/R/fun_getCodeSnippets.R b/program/shinyApp/R/fun_getCodeSnippets.R
@@ -1002,7 +1002,7 @@ if(numberOfScenario >= 14 & numberOfScenario <= 15){
 
   if(numberOfScenario == 15){
     stringtosave_1 <- '
-if(par_tmp$Enrichment$ValueToAttach == "LFC" | par_tmp$Enrichment$ValueToAttach == "LFC_abs" | input$ValueToAttach == "statistic_value"){
+if(par_tmp$Enrichment$ValueToAttach == "LFC" | par_tmp$Enrichment$ValueToAttach == "LFC_abs" | par_tmp$Enrichment$ValueToAttach == "statistic_value"){
   #get LFC
   ctrl_samples_idx <- which(colData(res_tmp$data)[,par_tmp$Enrichment$sample_annotation_types_cmp_GSEA] %in% par_tmp$Enrichment$Groups2Compare_ref_GSEA)
   comparison_samples_idx <- which(colData(res_tmp$data)[,par_tmp$Enrichment$sample_annotation_types_cmp_GSEA] %in% par_tmp$Enrichment$Groups2Compare_treat_GSEA)
@@ -1019,7 +1019,7 @@ if(par_tmp$Enrichment$ValueToAttach == "LFC" | par_tmp$Enrichment$ValueToAttach
   }
   else if(par_tmp$Enrichment$ValueToAttach == "LFC_abs"){
     geneSetChoice_tmp <- abs(Data2Plot_tmp$LFC)
-  } else if(input$ValueToAttach == "LFC_abs"){
+  } else if(par_tmp$Enrichment$ValueToAttach == "LFC_abs"){
     geneSetChoice_tmp <- abs(Data2Plot_tmp$LFC)
   }