From fb0874b2333e4e857bcfc8ae2fbaf9a6c32c803c Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Wed, 31 Jan 2024 11:49:14 +0100
Subject: [PATCH 1/5] Removed unhelpful comments

---
 program/shinyApp/R/significance_analysis/ui.R | 26 +++++++------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/program/shinyApp/R/significance_analysis/ui.R b/program/shinyApp/R/significance_analysis/ui.R
index a5e6257f..71ce992a 100644
--- a/program/shinyApp/R/significance_analysis/ui.R
+++ b/program/shinyApp/R/significance_analysis/ui.R
@@ -2,22 +2,17 @@ significance_analysis_sidebar_ui<- function(ns){
   sidebarPanel(
     id = "sidebar_significance_analysis",
     h5(" ") %>% helper(type = "markdown", content = "SigAna_Choices"),
-    # UI to choose type of comparison
     uiOutput(outputId = ns("type_of_comparison_ui")),
-    # UI to choose comparisons
     uiOutput(outputId = ns("chooseComparisons_ui")),
     # UI to choose test method
     uiOutput(outputId = ns("chooseTest_ui")),
-    # UI to choose significance level
     uiOutput(outputId = ns("chooseSignificanceLevel_ui")),
-    # UI to choose test correction
     uiOutput(outputId = ns("chooseTestCorrection_ui")),
     # Button to start analysis
     actionButton(
       inputId = ns("significanceGo"),
       label = "Get significance analysis"
-      ),
-    # Button to refresh the UI
+    ),
     hidden(actionButton(
       inputId = ns("refreshUI"),
       label = "Refresh UI"
@@ -30,34 +25,31 @@ significance_analysis_sidebar_ui<- function(ns){
 significance_analysis_main_ui <- function(ns){
   mainPanel(
     id = "main_significance_analysis",
-    # informative text, whether analysis was done or not
     htmlOutput(outputId = ns("significance_analysis_info"), container = pre),
     tabsetPanel(
       id = ns("significance_analysis_results"),
       tabPanel(
         title = "Result Visualization",
-        # UI for visualization Plot
         plotOutput(outputId = ns("Significant_Plot_final")),
         # UI to select comparisons to visualize
         splitLayout(  # Only used for questionmark
-            cellWidths = c("26%", "74%"),
-            h4("Visualization Choices") %>% helper(type = "markdown", content = "SigAna_Vis"),
-            NULL
+          cellWidths = c("26%", "74%"),
+          h4("Visualization Choices") %>% helper(type = "markdown", content = "SigAna_Vis"),
+          NULL
         ),
         uiOutput(outputId = ns("chooseComparisonsToVisualize_ui")),
-        # UI to choose visualization method
         uiOutput(outputId = ns("chooseVisualization_ui")),
-        # UI to choose what genes to llok at (e.g. significant, upregulated, downregulated)
+        # Choose what genes to look at (e.g. significant, upregulated, downregulated)
         uiOutput(outputId = ns("chooseGenesToLookAt_ui")),
         hr(style = "border-top: 1px solid #000000;"),
-        # UI to choose intersections to highlight
+        # Choose intersections to highlight
         h5(" ") %>% helper(type = "markdown", content = "SigAna_Intersections"),
         uiOutput(outputId = ns("chooseIntersections_ui")),
         # Download highlighted intersections as table
         downloadButton(
-            outputId = ns("downloadIntersections"),
-            label = "Download Intersections",
-            class = "btn-info"
+          outputId = ns("downloadIntersections"),
+          label = "Download Intersections",
+          class = "btn-info"
         ),
         # Download and Report UI
         splitLayout(

From ceeef2cfa00a355546e04e82ad4ec84c556cf1a0 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Wed, 31 Jan 2024 11:50:35 +0100
Subject: [PATCH 2/5] Removed updates as parameter

---
 program/shinyApp/R/significance_analysis/server.R | 5 +----
 program/shinyApp/server.R                         | 3 +--
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
index d88beafc..b646369c 100644
--- a/program/shinyApp/R/significance_analysis/server.R
+++ b/program/shinyApp/R/significance_analysis/server.R
@@ -1,4 +1,4 @@
-significance_analysis_server <- function(id, data, params, updates){
+significance_analysis_server <- function(id, data, params){
   moduleServer(
     id,
     function(input,output,session){
@@ -9,7 +9,6 @@ significance_analysis_server <- function(id, data, params, updates){
         dds = NULL,
         scenario = 0,
         comparisons_for_plot = "all",
-        current_updates = 0,
         coldata = NULL
       )
       ns <- session$ns
@@ -182,7 +181,6 @@ significance_analysis_server <- function(id, data, params, updates){
       observeEvent(input$refreshUI, {
         data <- update_data(session$token)
         params <- update_params(session$token)
-        sig_ana_reactive$current_updates <- updates()
         sig_ana_reactive$coldata <- colData(data$data)
       })
       # Analysis initial info
@@ -201,7 +199,6 @@ significance_analysis_server <- function(id, data, params, updates){
         print("Start the Significance Analysis")
         # update the data if needed
         data <- update_data(session$token)
-        sig_ana_reactive$current_updates <- updates()
         sig_ana_reactive$coldata <- colData(data$data)
         # delete old panels
         if(!is.null(significance_tabs_to_delete)){
diff --git a/program/shinyApp/server.R b/program/shinyApp/server.R
index 19b90836..5d0c1ccc 100644
--- a/program/shinyApp/server.R
+++ b/program/shinyApp/server.R
@@ -1091,8 +1091,7 @@ server <- function(input,output,session){
   significance_analysis_server(
     id = 'SignificanceAnalysis',
     data = res_tmp[[session$token]],
-    params = par_tmp[[session$token]],
-    reactive(updating$count)
+    params = par_tmp[[session$token]]
   )
   # PCA ----
   pca_Server(

From ca80617eff8a73166162e2d44b62aff035ae8569 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Thu, 1 Feb 2024 11:23:23 +0100
Subject: [PATCH 3/5] Removed some print statements. Made
 significance_tabs_to_delete into a reactive value.

---
 .../shinyApp/R/significance_analysis/server.R | 169 ++++++++----------
 .../shinyApp/R/significance_analysis/util.R   |   3 -
 2 files changed, 75 insertions(+), 97 deletions(-)

diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
index b646369c..229e8c68 100644
--- a/program/shinyApp/R/significance_analysis/server.R
+++ b/program/shinyApp/R/significance_analysis/server.R
@@ -9,7 +9,8 @@ significance_analysis_server <- function(id, data, params){
         dds = NULL,
         scenario = 0,
         comparisons_for_plot = "all",
-        coldata = NULL
+        coldata = NULL,
+        significance_tabs_to_delete = NULL
       )
       ns <- session$ns
       ## Sidebar UI section
@@ -28,7 +29,7 @@ significance_analysis_server <- function(id, data, params){
             multiple = F,
             selected = NULL
           )
-        } else{
+        } else {
           selectInput(
             inputId = ns("sample_annotation_types_cmp"),
             label = "Choose groups to compare",
@@ -37,7 +38,6 @@ significance_analysis_server <- function(id, data, params){
             selected = NULL
           )
         }
-
       })
       # UI to choose comparisons
       output$chooseComparisons_ui <- renderUI({
@@ -46,7 +46,7 @@ significance_analysis_server <- function(id, data, params){
         if(length(annoToSelect) == length(unique(annoToSelect))){
           # probably not what user wants, slows done app due to listing a lot of comparisons hence prevent
           helpText("unique elements, cant perform testing. Try to choose a different option at 'Choose the groups to show the data for'")
-        }else{
+        } else {
           my_comparisons <- subset(expand.grid(rep(list(unique(annoToSelect)),2)), Var1 != Var2)
           xy.list <- vector("list", nrow(my_comparisons))
           for (i in 1:nrow(my_comparisons)) {
@@ -71,7 +71,7 @@ significance_analysis_server <- function(id, data, params){
             expr = "DESeq is using a Wald test statistic.\nWe are using the same here.",
             outputArgs = list(container = pre)
           )
-        }else{
+        } else {
           shinyWidgets::virtualSelectInput(
             search = T,
             showSelectedOptionsFirst = T,
@@ -83,28 +83,24 @@ significance_analysis_server <- function(id, data, params){
         }
       })
       # UI to choose significance level
-      output$chooseSignificanceLevel_ui <- renderUI({
-        sliderInput(
-            inputId = ns("significance_level"),
-            label = "Significance level",
-            min = 0.005,
-            max = 0.1,
-            value = 0.05,
-            step = 0.005
-        )
-      })
+      output$chooseSignificanceLevel_ui <- renderUI({sliderInput(
+        inputId = ns("significance_level"),
+        label = "Significance level",
+        min = 0.005,
+        max = 0.1,
+        value = 0.05,
+        step = 0.005
+      )})
       # UI to choose test correction
-      output$chooseTestCorrection_ui <- renderUI({
-        selectInput(
-            inputId = ns("test_correction"),
-            label = "Test correction",
-            choices = c(
-              "None", "Bonferroni", "Benjamini-Hochberg", "Benjamini Yekutieli",
-              "Holm", "Hommel", "Hochberg", "FDR"
-            ),
-            selected = "Benjamini-Hochberg"
-        )
-      })
+      output$chooseTestCorrection_ui <- renderUI({selectInput(
+        inputId = ns("test_correction"),
+        label = "Test correction",
+        choices = c(
+          "None", "Bonferroni", "Benjamini-Hochberg", "Benjamini Yekutieli",
+          "Holm", "Hommel", "Hochberg", "FDR"
+        ),
+        selected = "Benjamini-Hochberg"
+      )})
       # UI to select comparisons to visualize
       output$chooseComparisonsToVisualize_ui <- renderUI({
         req(input$comparisons)
@@ -126,10 +122,10 @@ significance_analysis_server <- function(id, data, params){
           choices <- c("UpSetR plot")
         }
         selectInput(
-            inputId = ns("visualization_method"),
-            label = "Visualization method",
-            choices = choices,
-            selected = input$visualization_method
+          inputId = ns("visualization_method"),
+          label = "Visualization method",
+          choices = choices,
+          selected = input$visualization_method
         )
       })
       # UI to choose what genes to look at (e.g. significant, upregulated, downregulated)
@@ -137,23 +133,23 @@ significance_analysis_server <- function(id, data, params){
         req(input$comparisons_to_visualize)
         # choices dependent on preprocess_method
         if(params$PreProcessing_Procedure == "vst_DESeq"){
-            choices <- c(
-              "Significant",
-              "Upregulated",
-              "Downregulated",
-              "Significant unadjusted"
-            )
+          choices <- c(
+            "Significant",
+            "Upregulated",
+            "Downregulated",
+            "Significant unadjusted"
+          )
         } else {
-            choices <- c(
-              "Significant",
-              "Significant unadjusted"
-            )
+          choices <- c(
+            "Significant",
+            "Significant unadjusted"
+          )
         }
         selectInput(
-            inputId = ns("sig_to_look_at"),
-            label = "Type of significance to look at",
-            choices = choices,
-            selected = input$sig_to_look_at
+          inputId = ns("sig_to_look_at"),
+          label = "Type of significance to look at",
+          choices = choices,
+          selected = input$sig_to_look_at
         )
       })
       # ui to choose intersections to highlight in venn diagram
@@ -163,11 +159,11 @@ significance_analysis_server <- function(id, data, params){
         req(sig_ana_reactive$plot_last)
         choices <- append("None", sig_ana_reactive$intersect_names)
         selectInput(
-            inputId = ns("intersection_high"),
-            label = "Intersections to highlight",
-            choices = choices,
-            multiple = T,
-            selected = input$intersection_high
+          inputId = ns("intersection_high"),
+          label = "Intersections to highlight",
+          choices = choices,
+          multiple = T,
+          selected = input$intersection_high
         )
       })
       # keep updating the info panel while executing
@@ -185,44 +181,40 @@ significance_analysis_server <- function(id, data, params){
       })
       # Analysis initial info
       observeEvent(input$significanceGo,{
-        # shinyjs::html(id = 'significance_analysis_info', "Analysis is running...")
         sig_ana_reactive$info_text <- "Analysis is running..."
-        # start the analysis
         sig_ana_reactive$start_analysis <- sig_ana_reactive$start_analysis + 1
       })
       # Do the analysis
       observeEvent(sig_ana_reactive$start_analysis,{
         req(sig_ana_reactive$start_analysis > 0)
         if(input$significanceGo == 1){
-          significance_tabs_to_delete <<- NULL
+          sig_ana_reactive$significance_tabs_to_delete <- NULL
         }
         print("Start the Significance Analysis")
         # update the data if needed
         data <- update_data(session$token)
         sig_ana_reactive$coldata <- colData(data$data)
         # delete old panels
-        if(!is.null(significance_tabs_to_delete)){
-          for (i in 1:length(significance_tabs_to_delete)) {
+        if(!is.null(sig_ana_reactive$significance_tabs_to_delete)){
+          for (i in 1:length(sig_ana_reactive$significance_tabs_to_delete)) {
             removeTab(
               inputId = "significance_analysis_results",
-              target = significance_tabs_to_delete[[i]]
+              target = sig_ana_reactive$significance_tabs_to_delete[[i]]
             )
           }
         }
         # if preproccesing method was DESeq2, then use DESeq2 for testing
         if(params$PreProcessing_Procedure == "vst_DESeq"){
           dds <- data$DESeq_obj
-
           # rewind the comparisons again
           newList <- input$comparisons
           contrasts <- vector("list", length(input$comparisons))
-          for (i in 1:length(newList)) {
+          for (i in seq_along(newList)) {
             contrasts[[i]] <- unlist(strsplit(x = input$comparisons[i],split = ":"))
           }
-
           # get the results for each contrast and put it all in a big results object
           sig_results <<- list()
-          for (i in 1:length(contrasts)) {
+          for (i in seq_along(contrasts)) {
             if(identical(
               list(test_method = "Wald", test_correction = PADJUST_METHOD[[input$test_correction]]),
               par_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
@@ -246,15 +238,13 @@ significance_analysis_server <- function(id, data, params){
               test_method = "Wald",
               test_correction = PADJUST_METHOD[[input$test_correction]]
             )
-            ### put in here browser if use of `script_getSigToExcel`
           }
-        }
-        else{  # all other methods require manual testing
+        } else {  # all other methods require manual testing
           # rewind the comparisons again
           newList <- input$comparisons
           contrasts <- vector("list", length(input$comparisons))
           contrasts_all <- list()
-          for (i in 1:length(newList)) {
+          for (i in seq_along(newList)) {
             contrasts[[i]] <- unlist(strsplit(x = input$comparisons[i],split = ":"))
             contrasts_all <- append(contrasts_all, contrasts[[i]])
           }
@@ -289,7 +279,7 @@ significance_analysis_server <- function(id, data, params){
             ns = ns,
             preprocess_method = params$PreProcessing_Procedure
           )
-          significance_tabs_to_delete[[i]] <<- input$comparisons[i]
+          sig_ana_reactive$significance_tabs_to_delete[[i]] <- input$comparisons[i]
         }
         sig_ana_reactive$info_text <- "Analysis is Done!"
         # update plot
@@ -317,8 +307,7 @@ significance_analysis_server <- function(id, data, params){
         # assign scenario=20 for Venn Diagram and scenario=21 for UpSetR
         if(input$visualization_method == "Venn Diagram"){
           sig_ana_reactive$scenario <- 20
-        }
-        else{
+        } else {
           sig_ana_reactive$scenario <- 21
         }
         # get the results
@@ -334,10 +323,9 @@ significance_analysis_server <- function(id, data, params){
 
         if(any(input$comparisons_to_visualize == "all")){
           # show all comparisons if no more than 4
-          if(length(input$comparisons)<5){
+          if(length(input$comparisons) < 5){
             chosenVizSet <- input$comparisons
-          }else{
-
+          } else {
             chosenVizSet <-  input$comparisons[c(1,2)]
             sig_ana_reactive$info_text <- "Note: Although you choose 'all' to visualize only first 2 comparisons are shown to avoid unwanted computational overhead, 
             as you got more than 4 comparisons. Please choose precisely the comparisons for visualisation."
@@ -345,7 +333,7 @@ significance_analysis_server <- function(id, data, params){
         }else{
           chosenVizSet <- input$comparisons_to_visualize
         }
-        for (i in 1:length(chosenVizSet)) {
+        for (i in seq_along(chosenVizSet)) {
           to_add_tmp <- rownames(
             filter_significant_result(
               result = sig_results[[chosenVizSet[i]]],
@@ -362,12 +350,12 @@ significance_analysis_server <- function(id, data, params){
         if(length(res2plot) <= 1){
           sig_ana_reactive$info_text <- "You either have no significant results or only significant results in one comparison."
           # if current plots to llok at are adjusted pvalues, suggest to look at raw pvalues
-            if(input$sig_to_look_at == "Significant"){
-                sig_ana_reactive$info_text <- paste0(
+          if(input$sig_to_look_at == "Significant"){
+              sig_ana_reactive$info_text <- paste0(
                 sig_ana_reactive$info_text,
                 "\nYou tried to look at adjusted pvalues.\nYou might want to look at raw pvalues (CAUTION!) or change the significance level."
-                )
-            }
+              )
+          }
           # clear the plot
           output$Significant_Plot_final <- renderPlot({})
           return(NULL)
@@ -384,7 +372,7 @@ significance_analysis_server <- function(id, data, params){
           sig_ana_reactive$intersect_names <-  ggplot_build(
             sig_ana_reactive$plot_last
           )$layout$panel_params[[1]]$x$get_labels()
-        }else if(input$visualization_method == "Venn diagram"){
+        } else if(input$visualization_method == "Venn diagram"){
           # set colors for each comparison
           sig_ana_reactive$plot_last <- ggvenn::ggvenn(
             res2plot, fill_color=c("#44af69", "#f8333c", "#fcab10", "#2b9eb3"),
@@ -403,11 +391,6 @@ significance_analysis_server <- function(id, data, params){
           plot=sig_ana_reactive$plot_last,
           overlap_list=sig_ana_reactive$overlap_list
         )
-        querie_names <- map_intersects_for_highlight(
-          highlights=input$intersection_high,
-          plot=sig_ana_reactive$plot_last,
-          overlap_list=sig_ana_reactive$overlap_list
-        )
         queries <- vector("list", length(querie_names_all))
         for(i_querie in seq_along(sig_ana_reactive$intersect_names)){
           if(sig_ana_reactive$intersect_names[[i_querie]] %in% input$intersection_high){
@@ -470,8 +453,6 @@ significance_analysis_server <- function(id, data, params){
           write.csv(tosave, file, row.names = FALSE)
         }
       )
-
-
       # Download and Report Section
       # download R Code for further plotting
       output$getR_Code <- downloadHandler(
@@ -510,7 +491,6 @@ significance_analysis_server <- function(id, data, params){
           paste0(id, Sys.time(), input$file_ext_Sig)
         },
         content = function(file){
-          print("Plot saving.")
           ggsave(
             filename = file,
             plot = sig_ana_reactive$plot_last,
@@ -536,9 +516,9 @@ significance_analysis_server <- function(id, data, params){
           fun_LogIt(
             message = "- Significance Analysis was performed using DESeq2 pipeline"
           )
-        }else{
+        } else {
           fun_LogIt(message = paste(
-              "- Significance Analysis was performed using", input$test_method
+            "- Significance Analysis was performed using", input$test_method
           ))
         }
         # log the significance level
@@ -563,9 +543,10 @@ significance_analysis_server <- function(id, data, params){
             "- Number of significant genes after correction for",
             input$comparisons_to_visualize[i],
             "is",
-            nrow(sig_results[[input$comparisons_to_visualize[i]]][
-                   sig_results[[input$comparisons_to_visualize[i]]]$padj < input$significance_level,
-                 ]
+            nrow(
+              sig_results[[input$comparisons_to_visualize[i]]][
+                sig_results[[input$comparisons_to_visualize[i]]]$padj < input$significance_level,
+              ]
             )
           ))
           # log the number of significant genes before correction
@@ -573,9 +554,10 @@ significance_analysis_server <- function(id, data, params){
             "- Number of significant genes after correction for",
             input$comparisons_to_visualize[i],
             "is",
-            nrow(sig_results[[input$comparisons_to_visualize[i]]][
-                   sig_results[[input$comparisons_to_visualize[i]]]$pvalue < input$significance_level,
-                 ]
+            nrow(
+              sig_results[[input$comparisons_to_visualize[i]]][
+                sig_results[[input$comparisons_to_visualize[i]]]$pvalue < input$significance_level,
+              ]
             )
           ))
           # log the top 5 significant genes
@@ -587,7 +569,7 @@ significance_analysis_server <- function(id, data, params){
                 decreasing = FALSE
               ),], 5
             )
-          }else{
+          } else {
             # get the top 5 significant genes
             top5 <- head(
               sig_results[[input$comparisons_to_visualize[i]]][order(
@@ -600,8 +582,7 @@ significance_analysis_server <- function(id, data, params){
             "- Top 5 significant genes for",
             input$comparisons_to_visualize[i],
             "are the following:"
-            )
-          )
+          ))
           fun_LogIt(message = knitr::kable(
             top5, format = "html", format.args = list(width = 40)
           ) %>% kableExtra::kable_styling()
diff --git a/program/shinyApp/R/significance_analysis/util.R b/program/shinyApp/R/significance_analysis/util.R
index 9567073f..505450bf 100644
--- a/program/shinyApp/R/significance_analysis/util.R
+++ b/program/shinyApp/R/significance_analysis/util.R
@@ -38,9 +38,6 @@ create_new_tab_manual <- function(title, targetPanel, result, contrast, alpha, n
   # alpha: significance level
   # ns: namespace function
 
-  print("create_new_tab")
-  print(title)
-  print(result)
   # paste together the strings to print
   # total number of genes compared
   total_genes <- length(rownames(result))

From 0f141ecf50ed24e65bb51bd678f1e933b60f3013 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Thu, 1 Feb 2024 11:31:51 +0100
Subject: [PATCH 4/5] changed sig_result inot reactive instead of global
 variable.

---
 .../shinyApp/R/significance_analysis/server.R | 41 ++++++++++---------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
index 229e8c68..1d8cc082 100644
--- a/program/shinyApp/R/significance_analysis/server.R
+++ b/program/shinyApp/R/significance_analysis/server.R
@@ -10,7 +10,8 @@ significance_analysis_server <- function(id, data, params){
         scenario = 0,
         comparisons_for_plot = "all",
         coldata = NULL,
-        significance_tabs_to_delete = NULL
+        significance_tabs_to_delete = NULL,
+        sig_results = NULL
       )
       ns <- session$ns
       ## Sidebar UI section
@@ -213,17 +214,17 @@ significance_analysis_server <- function(id, data, params){
             contrasts[[i]] <- unlist(strsplit(x = input$comparisons[i],split = ":"))
           }
           # get the results for each contrast and put it all in a big results object
-          sig_results <<- list()
+          sig_ana_reactive$sig_results <<- list()
           for (i in seq_along(contrasts)) {
             if(identical(
               list(test_method = "Wald", test_correction = PADJUST_METHOD[[input$test_correction]]),
               par_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
             )){
               print("Results exists, skipping calculations.")
-              sig_results[[input$comparisons[i]]] <<- res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
+              sig_ana_reactive$sig_results[[input$comparisons[i]]] <<- res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
               next
             }
-            sig_results[[input$comparisons[i]]] <<- DESeq2::results(
+            sig_ana_reactive$sig_results[[input$comparisons[i]]] <<- DESeq2::results(
               dds,
               contrast = c(
                 input$sample_annotation_types_cmp,
@@ -233,7 +234,7 @@ significance_analysis_server <- function(id, data, params){
               pAdjustMethod = PADJUST_METHOD[[input$test_correction]]
             )
             # fill in res_tmp[[session$token]], par_tmp[[session$token]]
-            res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- sig_results[[input$comparisons[i]]]
+            res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- sig_ana_reactive$sig_results[[input$comparisons[i]]]
             par_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- list(
               test_method = "Wald",
               test_correction = PADJUST_METHOD[[input$test_correction]]
@@ -259,7 +260,7 @@ significance_analysis_server <- function(id, data, params){
           samples_selected <- colData(data$data)[index_comparisons,]
           # get the data
           data_selected <- as.matrix(assay(data$data))[,index_comparisons]
-          sig_results <<- significance_analysis(
+          sig_ana_reactive$sig_results <<- significance_analysis(
             df = as.data.frame(data_selected),
             samples = as.data.frame(samples_selected),
             contrasts = contrasts,
@@ -269,11 +270,11 @@ significance_analysis_server <- function(id, data, params){
           )
         }
         # for each result create a tabPanel
-        for (i in 1:length(sig_results)) {
+        for (i in seq_along(sig_ana_reactive$sig_results)) {
           create_new_tab(
             title = input$comparisons[i],
             targetPanel = "significance_analysis_results",
-            result = sig_results[[input$comparisons[i]]],
+            result = sig_ana_reactive$sig_results[[input$comparisons[i]]],
             contrast = contrasts[[i]],
             alpha = input$significance_level,
             ns = ns,
@@ -336,7 +337,7 @@ significance_analysis_server <- function(id, data, params){
         for (i in seq_along(chosenVizSet)) {
           to_add_tmp <- rownames(
             filter_significant_result(
-              result = sig_results[[chosenVizSet[i]]],
+              result = sig_ana_reactive$sig_results[[chosenVizSet[i]]],
               alpha = input$significance_level,
               filter_type = input$sig_to_look_at
             )
@@ -432,7 +433,7 @@ significance_analysis_server <- function(id, data, params){
           )
           intersect_set <- vector("list", length(intersects))
           intersect_name <- vector("list", length(intersects))
-          for(i_inter in 1:length(intersects)){
+          for(i_inter in seq_along(intersects)){
             # select dataframe for only comparisons considered in intersect
             df_inter <- as.data.frame(df[,intersects[[i_inter]]])  # as.data.frame for intersects of size 1
             rownames(df_inter) <- rownames(df)
@@ -461,7 +462,7 @@ significance_analysis_server <- function(id, data, params){
         },
         content = function(file){
           envList <- list(
-            sig_results = sig_results,
+            sig_results = sig_ana_reactive$sig_results,
             input = reactiveValuesToList(input),
             res2plot = sig_ana_reactive$results_for_plot
           )
@@ -536,7 +537,7 @@ significance_analysis_server <- function(id, data, params){
         ))
         # for each comparison, log the number of significant genes before and after correction
         # and the top 5 significant genes
-        for(i in 1:length(input$comparisons_to_visualize)){
+        for(i in seq_along(input$comparisons_to_visualize)){
            fun_LogIt(message = paste("####", input$comparisons_to_visualize[i]))
           # log the number of significant genes after correction
           fun_LogIt(message = paste(
@@ -544,8 +545,8 @@ significance_analysis_server <- function(id, data, params){
             input$comparisons_to_visualize[i],
             "is",
             nrow(
-              sig_results[[input$comparisons_to_visualize[i]]][
-                sig_results[[input$comparisons_to_visualize[i]]]$padj < input$significance_level,
+              sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]][
+                sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]]$padj < input$significance_level,
               ]
             )
           ))
@@ -555,8 +556,8 @@ significance_analysis_server <- function(id, data, params){
             input$comparisons_to_visualize[i],
             "is",
             nrow(
-              sig_results[[input$comparisons_to_visualize[i]]][
-                sig_results[[input$comparisons_to_visualize[i]]]$pvalue < input$significance_level,
+              sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]][
+                sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]]$pvalue < input$significance_level,
               ]
             )
           ))
@@ -564,16 +565,16 @@ significance_analysis_server <- function(id, data, params){
           if(params$PreProcessing_Procedure == "vst_DESeq"){
             # get the top 5 significant genes
             top5 <- head(
-              sig_results[[input$comparisons_to_visualize[i]]]@result[order(
-                sig_results[[input$comparisons_to_visualize[i]]]@result$p.adjust,
+              sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]]@result[order(
+                sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]]@result$p.adjust,
                 decreasing = FALSE
               ),], 5
             )
           } else {
             # get the top 5 significant genes
             top5 <- head(
-              sig_results[[input$comparisons_to_visualize[i]]][order(
-                sig_results[[input$comparisons_to_visualize[i]]]$padj,
+              sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]][order(
+                sig_ana_reactive$sig_results[[input$comparisons_to_visualize[i]]]$padj,
                 decreasing = FALSE
               ),], 5
             )

From f063be663a95c15cc58390e1802b70d56b4979e5 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Thu, 1 Feb 2024 11:32:25 +0100
Subject: [PATCH 5/5] Removed a warning my pycharm.

---
 program/shinyApp/R/significance_analysis/server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
index 1d8cc082..d109a21a 100644
--- a/program/shinyApp/R/significance_analysis/server.R
+++ b/program/shinyApp/R/significance_analysis/server.R
@@ -197,7 +197,7 @@ significance_analysis_server <- function(id, data, params){
         sig_ana_reactive$coldata <- colData(data$data)
         # delete old panels
         if(!is.null(sig_ana_reactive$significance_tabs_to_delete)){
-          for (i in 1:length(sig_ana_reactive$significance_tabs_to_delete)) {
+          for (i in seq_along(sig_ana_reactive$significance_tabs_to_delete)) {
             removeTab(
               inputId = "significance_analysis_results",
               target = sig_ana_reactive$significance_tabs_to_delete[[i]]