Fixed error of deleting report events

ICB-DCM · Jan 30, 2025 · f741580 · f741580
1 parent d51041b
commit f741580
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Showing 2 changed files with 54 additions and 47 deletions.
diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
@@ -39,11 +39,11 @@ significance_analysis_server <- function(id, data, params){
             sig_ana_reactive$coldata <- colData(data$data)
           }
           req(sig_ana_reactive$coldata)
-          if(params$PreProcessing_Procedure == "vst_DESeq"){
+          if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
             selectInput(
               inputId = ns("sample_annotation_types_cmp"),
               label = "Choose groups to compare",
-              choices = params$DESeq_factors,
+              choices = par_tmp[[session$token]]$DESeq_factors,
               multiple = F,
               selected = NULL
             )
@@ -84,7 +84,7 @@ significance_analysis_server <- function(id, data, params){
         })
         # UI to choose test method
         output$chooseTest_ui <- renderUI({
-          if(params$PreProcessing_Procedure == "vst_DESeq"){
+          if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
             renderText(
               expr = "DESeq is using a Wald test statistic.\nWe are using the same here.",
               outputArgs = list(container = pre)
@@ -131,7 +131,7 @@ significance_analysis_server <- function(id, data, params){
         output$chooseGenesToLookAt_ui <- renderUI({
           req(input$comparisons_to_visualize)
           # choices dependent on preprocess_method
-          if(params$PreProcessing_Procedure == "vst_DESeq"){
+          if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
             choices <- c(
               "Significant",
               "Upregulated",
@@ -246,7 +246,7 @@ significance_analysis_server <- function(id, data, params){
           }
         }
         # if preproccesing method was DESeq2, then use DESeq2 for testing
-        if(params$PreProcessing_Procedure == "vst_DESeq"){
+        if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
           if (useBatch){
             dds <- data$DESeq_obj_batch_corrected
           } else {
@@ -570,7 +570,7 @@ significance_analysis_server <- function(id, data, params){
 
           )
 
-          if(params$PreProcessing_Procedure == "vst_DESeq"){
+          if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
             envList$dds <- data$DESeq_obj
           }
           temp_directory <- file.path(tempdir(), as.integer(Sys.time()))
@@ -643,7 +643,7 @@ significance_analysis_server <- function(id, data, params){
         fun_LogIt(message = "## Differential analysis {.tabset .tabset-fade}")
         fun_LogIt(message = "### Info")
         # log which tests were performed
-        if(params$PreProcessing_Procedure == "vst_DESeq"){
+        if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq"){
           fun_LogIt(
             message = "- Differential Analysis was performed using DESeq2 pipeline"
           )
@@ -692,7 +692,7 @@ significance_analysis_server <- function(id, data, params){
             )
           ))
           # log the top 5 significant genes
-          if(params$PreProcessing_Procedure == "vst_DESeq" & "result" %in% names(sig_ana_reactive$sig_results[[comparisons[i]]])){
+          if(par_tmp[[session$token]]$PreProcessing_Procedure == "vst_DESeq" & "result" %in% names(sig_ana_reactive$sig_results[[comparisons[i]]])){
             top5 <- head(
                 sig_ana_reactive$sig_results[[comparisons[i]]]@result[order(
                   sig_ana_reactive$sig_results[[comparisons[i]]]@result$p.adjust,

diff --git a/program/shinyApp/R/significance_analysis/util.R b/program/shinyApp/R/significance_analysis/util.R
@@ -709,22 +709,22 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
             h5("Volcano plot padj"),
             h5("Both Volcano plots"),
             h5("Volcano plot pvalue")
-          ),
+          ) %>% helper(type = "markdown", content = "SampleCorr_Downloads"),
           splitLayout(
             style = "border: 1px solid silver:",
             cellWidths = c("35%","35%", "30%"),
             actionButton(
-              inputId = ns("only2Report_Volcano"),
+              inputId = ns(paste(contrast[1], contrast[2], "only2Report_Volcano", sep = "_")),
               label = "Send only to Report",
               class = "btn-info"
             ),
             actionButton(
-              inputId = ns("only2Report_Volcano_both"),
+              inputId = ns(paste(contrast[1], contrast[2], "only2Report_Volcano_both", sep = "_")),
               label = "Send only to Report",
               class = "btn-info"
             ),
             actionButton(
-              inputId = ns("only2Report_Volcano_raw"),
+              inputId = ns(paste(contrast[1], contrast[2], "only2Report_Volcano_raw", sep = "_")),
               label = "Send only to Report",
               class = "btn-info"
             )
@@ -737,11 +737,7 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
               label = "Get underlying R code and data",
               icon = icon("code")
             ),
-            downloadButton(
-              outputId = ns("getR_Code_Volcano_both"),
-              label = "Get underlying R code and data",
-              icon = icon("code")
-            ),
+            NULL,
             downloadButton(
               outputId = ns("getR_Code_Volcano_raw"),
               label = "Get underlying R code and data",
@@ -980,38 +976,49 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
   })
 
   # downloadhandlers
-  observeEvent(input[[ns("only2Report_Volcano")]],{
-    fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
-    fun_LogIt(message = "### Info")
-    log_messages_volcano(
-      sig_ana_reactive$VolcanoPlot + theme(legend.position = "right"),
-      sig_ana_reactive$data4Volcano,
-      contrast, file_path
-    )
-    fun_LogIt(message = "### Publication Snippet")
-    fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
-                                       params = par_tmp[[session$token]]))
-  })
+  session$userData[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano", sep = "_"))]] <- observeEvent(
+    input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano", sep = "_"))]], {
+      if(!is.null(session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_val", sep = "_")]])){
+          req(input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano", sep = "_"))]] > session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_val", sep = "_")]])
+      }
+      fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
+      fun_LogIt(message = "### Info")
+      log_messages_volcano(sig_ana_reactive$VolcanoPlot, sig_ana_reactive$data4Volcano, contrast, file_path)
+      fun_LogIt(message = "### Publication Snippet")
+      fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
+                                         params = par_tmp[[session$token]]))
+    }
+  )
 
-  observeEvent(input[[ns("only2Report_Volcano_both")]],{
-    fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
-    fun_LogIt(message = "### Info")
-    log_messages_volcano(gridExtra::arrangeGrob(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$VolcanoPlot)
-                         , sig_ana_reactive$data4Volcano, contrast, file_path)
-   # log_messages_volcano(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$data4Volcano, contrast, file_path)
-    fun_LogIt(message = "### Publication Snippet")
-    fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
-                                       params = par_tmp[[session$token]]))
-  })
+  session$userData[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_both", sep = "_"))]] <- observeEvent(
+    input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_both", sep = "_"))]],{
+      if(!is.null(session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_both_val", sep = "_")]])){
+        req(input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_both", sep = "_"))]] > session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_both_val", sep = "_")]])
+      }
+      fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
+      fun_LogIt(message = "### Info")
+      log_messages_volcano(gridExtra::arrangeGrob(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$VolcanoPlot),
+                           sig_ana_reactive$data4Volcano, contrast, file_path)
+      #log_messages_volcano(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$data4Volcano, contrast, file_path)
+      fun_LogIt(message = "### Publication Snippet")
+      fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
+                                         params = par_tmp[[session$token]]))
+    }
+  )
 
-  observeEvent(input[[ns("only2Report_Volcano_raw")]],{
-    fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
-    fun_LogIt(message = "### Info")
-    log_messages_volcano(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$data4Volcano, contrast, file_path)
-    fun_LogIt(message = "### Publication Snippet")
-    fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
-                                       params = par_tmp[[session$token]]))
-  })
+  session$userData[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_raw", sep = "_"))]] <- observeEvent(
+    input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_raw", sep = "_"))]],{
+      if(!is.null(session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_raw_val", sep = "_")]])){
+        req(input[[ns(paste(contrast[1], contrast[2], "only2Report_Volcano_raw", sep = "_"))]] > session$userData[[paste(contrast[1], contrast[2], "only2Report_Volcano_raw_val", sep = "_")]])
+      }
+      fun_LogIt(message = "## Differential analysis - Volcano {.tabset .tabset-fade}")
+      fun_LogIt(message = "### Info")
+      log_messages_volcano(sig_ana_reactive$VolcanoPlot_raw, sig_ana_reactive$data4Volcano, contrast, file_path)
+      fun_LogIt(message = "### Publication Snippet")
+      fun_LogIt(message = snippet_SigAna(data = res_tmp[[session$token]],
+                                         params = par_tmp[[session$token]]))
+    }
+  )
 
   output[[ns("getR_Code_Volcano")]] <- downloadHandler(
     filename = function(){