Merge branch 'develop' into show_codeGeneration_process

docs/interface-details/pre-processing.md

@@ -13,10 +13,10 @@ The Pre-processing tab is divided into two main sections: the side panel and the
 
 In the side panel, you have the following options:
 
--   **Pre-Processing Procedures**: You can select from various pre-processing procedures.
 
-    -   Options: none, filterOnly, vst_DESeq, simpleCenterScaling, Scaling_0_1, log10, pareto_scaling, ln
-    -   vst_DESeq also requires the selection of a design formula.
+- **Pre-Processing Procedures**: You can select from various pre-processing procedures.
+  - Options: none, filterOnly, vst_DESeq, simpleCenterScaling, Scaling_0_1, log10, log2, pareto_scaling, ln
+  - vst_DESeq also requires the selection of a design formula.
 
 -   **Select Batch Effect Column**: Choose a batch effect if applicable. Possible choices are taken from the sample annotation columns.
 

program/shinyApp/R/C.R

@@ -34,15 +34,15 @@ MANUALLY <- FALSE # change to TRUE, if you want to set the paths manually
 
 if(MANUALLY){
   # Adjust the path to the data file
-  envList <- readRDS('path/to/Data.rds')
+  envList <- readRDS('path/to/Data.RDS')
   # Adjust the path to the utils.R file
   source('path/to/utils.R')
   print('Path manually set')
 }else{
   # if you get an error try to set paths manually
   # remember to set MANUALLY <- TRUE
   direcoty_of_files <- dirname(rstudioapi::getSourceEditorContext()$path)
-  envList <- readRDS(paste0(direcoty_of_files,'/','Data.rds'))
+  envList <- readRDS(paste0(direcoty_of_files,'/','Data.RDS'))
   if('utils.R' %in% list.files(direcoty_of_files)){
     source(file.path(direcoty_of_files,'utils.R'))
   }
@@ -220,21 +220,21 @@ CUSTOM_THEME <<- theme_bw(base_size = 15) +
     plot.title = element_text(size = 17, face = "bold")  # Plot title
   )
 
-
-
-LOADING_SCREEN <<- tagList(
+LOADING_SCREEN <- tagList(
   div(
-    style = "position: relative; display: flex; justify-content: center; align-items: center;",
-    div(
-      style = "display: flex;",
-      img(src = "bored_panda_11.png", style = "max-width: 100%; height: auto;"),
-      img(src = "bored_panda_12.png", style = "max-width: 100%; height: auto;")
-    ),
+    style = "position: fixed; top: 0; left: 0; width: 100vw; height: 100vh; display: flex; justify-content: center; align-items: center; padding: 0; margin: 0; box-sizing: border-box; overflow: hidden; background-color: rgba(225, 225, 225, 0.5);", # Light background color
     div(
-      style = "position: absolute; top: 20%; left: 60%; transform: translate(-50%, -50%); display: flex; flex-direction: column; align-items: center; color: white; font-size: 24px; font-weight: bold;",
-      spin_flower(),
-      span("Computing...")
+      style = "display: flex; flex-direction: column; align-items: center; width: auto; height: auto; padding: 20px; margin: 0; box-sizing: border-box; background-color: rgba(225, 225, 225, 0); border-radius: 10px;", # Slightly darker background behind images
+      # Centered Images
+      img(src = "bored_panda_11.png", style = "width: 50%; height: auto; object-fit: contain; margin-bottom: 10px; padding: 0;"),
+      img(src = "bored_panda_12.png", style = "width: 50%; height: auto; object-fit: contain; margin: 0; padding: 0;"),
+
+      # Centered Spinner and Text
+      div(
+        style = "position: absolute; top: 50%; left: 50%; transform: translate(-50%, -50%); display: flex; flex-direction: column; align-items: center; color: white; font-size: 24px; font-weight: bold;",
+        spin_flower(),
+        span("Computing...")
+      )
     )
   )
-)
-
+)

program/shinyApp/R/Report_text_snippets.R

@@ -80,6 +80,8 @@ snippet_preprocessing <- function(
     snippet <- paste0(snippet, "The base-10 logarithm of each data point was calculated. If a single zero value was present, 1 was added to all points to avoid undefined results.\n")
   } else if (params$PreProcessing_Procedure == "ln") {
     snippet <- paste0(snippet, "The natural logarithm of each data point was calculated. If a single zero value was present, 1 was added to all points to avoid undefined results.\n")
+  } else if (params$PreProcessing_Procedure == "log2") {
+    snippet <- paste0(snippet, "The base-2 logarithm of each data point was calculated. If a single zero value was present, 1 was added to all points to avoid undefined results.\n")
   } else if (params$PreProcessing_Procedure == "pareto_scaling") {
     snippet <- paste0(snippet, "The data was parteo scaled. Pareto scaling emphasizes the importance of small values by dividing each data point by the square root of its standard deviation.\n")
   } else if(params$PreProcessing_Procedure == "None") {

program/shinyApp/R/data_selection/ui.R

@@ -119,7 +119,7 @@ data_selection_sidebar_panel <- sidebarPanel(
             selectInput(
               inputId = "omic_type_testdata",
               label = "Omic Type that is uploaded",
-              choices = c("Transcriptomics", "Lipidomics", "Metabolomics"),
+              choices = c("Transcriptomics"),
               selected = "",
               width = "80%"
             )

program/shinyApp/R/enrichment_analysis/server.R

@@ -496,7 +496,6 @@ enrichment_analysis_Server <- function(id, data, params, updates){
       observeEvent(input$enrichmentGO,{
         ea_reactives$ea_info <- "Enrichment is running..."
         waiter <- Waiter$new(
-          id=ns("EnrichmentTabs"),
           html = LOADING_SCREEN,
           color="#70BF4F47"
         )

program/shinyApp/R/fun_getCodeSnippets.R

@@ -235,7 +235,7 @@ lapply(ls(pattern="violin"), get)
 pca <- prcomp(
   x = as.data.frame(t(assay(res_tmp$data))),
   center = T,
-  scale. = FALSE
+  scale. = ifelse(par_tmp$PCA$scale_data == "Yes",T,F)
 )
     
 pcaData <- data.frame(pca$x,colData(res_tmp$data))

program/shinyApp/R/heatmap/server.R

@@ -136,7 +136,6 @@ heatmap_server <- function(id, data, params, updates){
         )
         req(selectedData_processed())
         waiter <- Waiter$new(
-          id=ns("HeatmapPlot"),
           html = LOADING_SCREEN,
           color="#70BF4F47"
         )

program/shinyApp/R/pca/server.R

@@ -130,7 +130,8 @@ pca_Server <- function(id, data, params, row_select){
         check <- check_calculations(list(
           sample_selection_pca = input$sample_selection_pca,
           SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca,
-          batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F)
+          batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F),
+          scale_data = input$scale_data
         ), "PCA")
         if (check == "No Result yet"){
           output$PCA_Info <- renderText("PCA computed.")
@@ -157,7 +158,6 @@ pca_Server <- function(id, data, params, row_select){
         req(data$data)
         req(input$Do_PCA[1] > 0)
         waiter <- Waiter$new(
-          id="plot_panels_pca",
           html = LOADING_SCREEN,
           color="#70BF4F47"
         )
@@ -200,7 +200,7 @@ pca_Server <- function(id, data, params, row_select){
             pca <- prcomp(
               x = as.data.frame(t(as.data.frame(assay(data2plot)))),
               center = T,
-              scale. = FALSE
+              scale. = ifelse(input$scale_data == "Yes",T,F)
             )
           }, error = function(e){
             error_modal(e)
@@ -223,7 +223,9 @@ pca_Server <- function(id, data, params, row_select){
           # assign par_temp as empty list
           par_tmp[[session$token]][["PCA"]] <<- list(
             sample_selection_pca = input$sample_selection_pca,
-            SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca
+            SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca,
+            batch = ifelse(par_tmp[[session$token]]$BatchColumn != "NULL" && input$UseBatch == "Yes",T,F),
+            scale_data = input$scale_data
           )
         } else {
           # otherwise read the reactive values

program/shinyApp/R/pca/ui.R

@@ -16,6 +16,14 @@ pca_sidebar_panel <- function(ns){
     ),
     uiOutput(outputId = ns("SampleAnnotationTypes_pca_ui")),
     uiOutput(outputId = ns("sample_selection_pca_ui")),
+    # Scale data to unit variance y/n
+    radioGroupButtons(
+      inputId = ns("scale_data"),
+      label = "Scale data to unit variance?",
+      choices = c("Yes","No"),
+      direction = "horizontal",
+      selected = "No"
+    ),
     ### start pca ---
     actionButton(
       inputId = ns("Do_PCA"),

program/shinyApp/R/pre_processing/ui.R

@@ -14,6 +14,7 @@ pre_processing_sidebar_panel <- sidebarPanel(
       "centering to 0 and scaling" = "simpleCenterScaling",
       "scaling values to be within 0 and 1" = "Scaling_0_1",
       "log10" = "log10",
+      "log2" = "log2",
       "Pareto scaling (mean-centered and scaled by the square root of the standard deviation)" = "pareto_scaling",
       "natural logarithm" = "ln"
     ),

program/shinyApp/R/pre_processing/util.R

@@ -10,7 +10,7 @@ preprocessing <- function(data, omic_type, procedure){
   if(procedure %in% c("Scaling_0_1", "pareto_scaling")){
     return(scaling_normalisation(data, omic_type, procedure))
   }
-  if(procedure %in% c("log10", "ln")){
+  if(procedure %in% c("log10", "ln", "log2")){
     return(ln_normalisation(data, omic_type, procedure))
   }
   if(procedure == "none"){
@@ -72,7 +72,18 @@ scaling_normalisation <- function(data, omic_type, scaling_procedure){
 
 ln_normalisation <- function(data, omic_type, logarithm_procedure){
   # Center and scale the data
-  logarithm <- ifelse(logarithm_procedure == "log10", log10, log)
+  if(logarithm_procedure == "log10")
+  {
+    logarithm = log10
+  }
+  else if(logarithm_procedure == "log2")
+  {
+    logarithm = log2
+  }
+  else
+  {
+    logarithm = log
+  }
   # prefilter the data
   data <- prefiltering(data, omic_type)
   # log the data and always add 1 to avoid -Inf

program/shinyApp/R/sample_correlation/server.R

@@ -50,7 +50,6 @@ sample_correlation_server <- function(id, data, params){
         req(input$SampleAnnotationChoice)
         req(input$Do_SampleCorrelation > 0)
         waiter <- Waiter$new(
-          id=ns("SampleCorrelationPlot"),
           html = LOADING_SCREEN,
           color="#A208BA35"
         )

program/shinyApp/R/significance_analysis/server.R

@@ -196,7 +196,6 @@ significance_analysis_server <- function(id, data, params){
       observeEvent(sig_ana_reactive$start_analysis,{
         req(sig_ana_reactive$start_analysis > 0)
         waiter <- Waiter$new(
-          id=ns("significance_analysis_results"),
           html = LOADING_SCREEN,
           color="#70BF4F47",
           hide_on_render=F

program/shinyApp/helpfiles/PreProcessing_Procedures.md

@@ -55,7 +55,13 @@
   - Special consideration is given to handling zero values to avoid undefined 
     results: If any zero values are present, +1 is added to all values before applying
     the logarithm.
-
+
+- **Logarithm Base 2 (log2):**
+  - The base-2 logarithm of each data point is calculated.
+  - Special consideration is given to handling zero values to avoid undefined 
+    results: If any zero values are present, +1 is added to all values before applying
+    the logarithm.
+
 - **Pareto Scaling:**
   - Pareto scaling emphasizes the importance of small values by dividing each data point by the square root of its standard deviation.
   - This method is suitable for datasets with a wide range of values.

program/shinyApp/server.R

@@ -495,11 +495,18 @@ server <- function(input,output,session){
     )){
       output$debug <- renderText("The Upload has failed, or you haven't uploaded anything yet")
     } else if (uploaded_from() == "testdata"){
+      show_toast(
+        title = paste(par_tmp[[session$token]]['omic_type'],"Example Upload"),
+        text = paste(par_tmp[[session$token]]['omic_type'],"- Example upload was successful"),
+        position = "top",
+        timer = 1500,
+        timerProgressBar = T
+      )
       output$debug <- renderText({"The Test Data Set was used"})
     } else {
       show_toast(
         title = paste(par_tmp[[session$token]]['omic_type'],"Data Upload"),
-        text = paste(par_tmp[[session$token]]['omic_type'],"-data upload was successful"),
+        text = paste(par_tmp[[session$token]]['omic_type'],"- data upload was successful"),
         position = "top",
         timer = 1500,
         timerProgressBar = T
@@ -528,6 +535,7 @@ server <- function(input,output,session){
 
       }
       showTab(inputId = "tabsetPanel1", target = "Pre-processing")
+
     }
   })
 
@@ -680,7 +688,6 @@ server <- function(input,output,session){
       "Number. of anno options annotation_rows lost: ",
       nrow(res_tmp[[session$token]]$data_original) - nrow(res_tmp[[session$token]]$data)
     ))
-
     return("DataUploadSuccesful")
   })
   #data_input_shiny = is the res object now which is global => not needed ?!
@@ -910,6 +917,7 @@ server <- function(input,output,session){
       html = LOADING_SCREEN,
       color = "#3897F147",
       hide_on_render = FALSE
+
     )
     waiter$show()
     print("Do Preprocessing")