From 414e0c1f99bdb99915a47b2c2d908412b136e242 Mon Sep 17 00:00:00 2001
From: Bernd Jagla <bernd.jagla@pasteur.fr>
Date: Wed, 10 Apr 2024 16:02:28 +0200
Subject: [PATCH] allow more levels

---
 DESCRIPTION          |  2 +-
 inst/app/outputs.R   |  9 ++++++++-
 inst/app/reactives.R | 25 ++++++++++++++++++-------
 3 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 27fb45bd..a10993b4 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SCHNAPPs
 Type: Package
 Title: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
-Version: 1.15.15
+Version: 1.15.16
 Authors@R: c(person("Bernd", "Jagla", role = c("aut", "cre"), email = "bernd.jagla@pasteur.fr", comment = c(ORCID = "0000-0002-7696-0484")))
 Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr>
 Description: Single Cell sHiny APPlication (SCHNAPPs) is a R/Shiny based application to interact, manipulate, explore, and analyze single cell RNA-seq experiments, including MARS-seq and others.
diff --git a/inst/app/outputs.R b/inst/app/outputs.R
index 8683bc64..a350e926 100644
--- a/inst/app/outputs.R
+++ b/inst/app/outputs.R
@@ -811,7 +811,14 @@ output$ColorSelection <- renderUI({
   # where and how to store the colors
   tabs= lapply(names(projections), FUN = function(name){
     if(is.factor(projections[,name])){
-      if(length(levels(projections[,name]))>30) return(NULL)
+      if(length(levels(projections[,name]))>100) {
+        showNotification(
+          paste(name," has more than 100 levels\n"),
+          type = "error",
+          duration = NULL
+        )
+        return(NULL)
+      }
       return(tmpFun(name = name, value = paste0(name, "ColorPanel"), lev = levels(projections[,name]), idStr = paste0(name, ".col."),
                     sampCol = defaultValue(paste0(name, ".colVec"), allowedColors[seq(levels(projections[,name]))]),
                     allowedColors = allowedColors)
diff --git a/inst/app/reactives.R b/inst/app/reactives.R
index ae66c09d..42a92d6d 100644
--- a/inst/app/reactives.R
+++ b/inst/app/reactives.R
@@ -406,7 +406,7 @@ inputDataFunc <- function(inFile) {
   if (.schnappsEnv$DEBUGSAVE) {
     save(file = "~/SCHNAPPsDebug/readInp.RData", list = c(ls()))
   }
-  # load(file='~/SCHNAPPsDebug/readInp.RData')
+  # cp =load(file='~/SCHNAPPsDebug/readInp.RData')
   
   
   #' save orginial data
@@ -3658,13 +3658,18 @@ inputSample <- reactive({
   if (.schnappsEnv$DEBUGSAVE) {
     save(file = "~/SCHNAPPsDebug/inputSample.RData", list = c(ls()))
   }
-  # load(file='~/SCHNAPPsDebug/inputSample.RData')
-  
+  # cp=load(file='~/SCHNAPPsDebug/inputSample.RData')
+  if(!"sampleNames" %in% colnames(colData(scEx))){
+    if (!is.null(getDefaultReactiveDomain())) {
+      showNotification("no sampleNames in colData(scEx)", id = "inputSampleErr", duration = NULL)
+      return(NULL)
+    }
+  }
   # TODO should come from sampleInfo
-  sampInf <- gsub(".*-(.*)", "\\1", scEx$barcode)
+  # sampInf <- gsub(".*-(.*)", "\\1", scEx$barcode)
   cellIds <- data.frame(
     cellName = colnames(scEx),
-    sample = sampInf,
+    sample = colData(scEx)$sampleNames,
     # number of genes per cell
     ngenes = Matrix::colSums(assays(scEx)[[1]]>0),
     nUMI = Matrix::colSums(assays(scEx)[[1]])
@@ -3707,12 +3712,18 @@ inputSampleOrg <- reactive({
     save(file = "~/SCHNAPPsDebug/inputSample.RData", list = c(ls()))
   }
   # load(file='~/SCHNAPPsDebug/inputSample.RData')
+  if(!"sampleNames" %in% colnames(colData(scEx))){
+    if (!is.null(getDefaultReactiveDomain())) {
+      showNotification("no sampleNames in colData(scEx)", id = "inputSampleErr", duration = NULL)
+      return(NULL)
+    }
+  }
   
   # TODO should come from sampleInfo
-  sampInf <- gsub(".*-(.*)", "\\1", dataTables$scEx$barcode)
+  # sampInf <- gsub(".*-(.*)", "\\1", dataTables$scEx$barcode)
   cellIds <- data.frame(
     cellName = colnames(dataTables$scEx),
-    sample = sampInf,
+    sample = colData(dataTables$scEx)$sampleNames,
     # number of genes per cell
     ngenes = Matrix::colSums(assays(dataTables$scEx)[[1]]>0),
     nUMI = Matrix::colSums(assays(dataTables$scEx)[[1]])