From 59e232ef88e45c93b81f571609fb480ce8088444 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Wed, 23 Oct 2024 15:37:05 +0200
Subject: [PATCH 1/3] Add option whether to scale data to unit variance

---
 program/shinyApp/R/pca/server.R | 9 ++++++---
 program/shinyApp/R/pca/ui.R     | 8 ++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/program/shinyApp/R/pca/server.R b/program/shinyApp/R/pca/server.R
index 07d7b071..72c5dc34 100644
--- a/program/shinyApp/R/pca/server.R
+++ b/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.")
@@ -200,7 +201,7 @@ 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$scale_data == "Yes",T,F)
             )
           }, error = function(e){
             error_modal(e)
@@ -223,7 +224,9 @@ pca_Server <- function(id, data, params, row_select){
           # assign par_temp as empty list
           par_tmp[[session$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
diff --git a/program/shinyApp/R/pca/ui.R b/program/shinyApp/R/pca/ui.R
index 9ac3835b..2e3e8227 100644
--- a/program/shinyApp/R/pca/ui.R
+++ b/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"),

From 58e1e2e9e9cf323bf046d6610179bed01507961b Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Wed, 23 Oct 2024 15:39:49 +0200
Subject: [PATCH 2/3] Added it to downloadable code

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

diff --git a/program/shinyApp/R/fun_getCodeSnippets.R b/program/shinyApp/R/fun_getCodeSnippets.R
index fbff02a9..35805a4d 100644
--- a/program/shinyApp/R/fun_getCodeSnippets.R
+++ b/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))

From a26c6fc8c024998fb1a30a85ac1b0625aa4cb000 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Wed, 23 Oct 2024 15:44:33 +0200
Subject: [PATCH 3/3] Fixed small error regarding rds vs RDS files in code

---
 program/shinyApp/R/C.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/program/shinyApp/R/C.R b/program/shinyApp/R/C.R
index 8e448533..b053fec0 100644
--- a/program/shinyApp/R/C.R
+++ b/program/shinyApp/R/C.R
@@ -34,7 +34,7 @@ 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')
@@ -42,7 +42,7 @@ if(MANUALLY){
   # 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'))
   }