bf processSeuratObject calling suPlotVariableFeatures

R/Seurat.Utils.R

@@ -141,24 +141,21 @@ processSeuratObject <- function(obj, param.list = p, add.meta.fractions = FALSE,
   if (plot) {
     message("------------------- Plotting -------------------")
 
-    res.ident <- paste0(DefaultAssay(obj), "_snn_res.", resolutions)[1:4]
-    print(res.ident)
-    message("qClusteringUMAPS: ", paste(res.ident))
-    qClusteringUMAPS(obj = obj, idents = res.ident)
-
+    try(suPlotVariableFeatures(obj = obj, assay = "RNA"), silent = TRUE)
 
     message("scPlotPCAvarExplained")
-    scPlotPCAvarExplained(obj)
+    try(scPlotPCAvarExplained(obj), silent = TRUE)
 
     message("qQC.plots.BrainOrg")
-    qQC.plots.BrainOrg(obj = obj)
+    try(qQC.plots.BrainOrg(obj = obj), silent = TRUE)
 
     # message("multi_clUMAP.A4")
     # multi_clUMAP.A4(obj = obj)
 
-    "HERE"
-    message("suPlotVariableFeatures")
-    suPlotVariableFeatures(obj = obj)
+    res.ident <- paste0(DefaultAssay(obj), "_snn_res.", resolutions)[1:4]
+    message("qClusteringUMAPS: ", paste(res.ident))
+    try(qClusteringUMAPS(obj = obj, idents = res.ident), silent = TRUE)
+
 
     if (ncol(obj) < 50000) { # TEMP
       message("qMarkerCheck.BrainOrg")
@@ -178,7 +175,6 @@ processSeuratObject <- function(obj, param.list = p, add.meta.fractions = FALSE,
       `Mesenchyme` = "DCN", Glycolytic = "PDK1",
       `Choroid.Plexus` = "OTX2", `Mesenchyme` = "DCN"
     )
-    message("plotQUMAPsInAFolder")
     try(plotQUMAPsInAFolder(genes = Signature.Genes.Top20, obj = obj), silent = TRUE)
   }
   tictoc::toc()
@@ -5440,7 +5436,6 @@ compareVarFeaturesAndRanks <- function(
   func_slot <- grepv(x = names(obj@commands), pattern = "^ScaleData")
   message("Slot: ", paste(func_slot))
 
-
   if(is.null(func_slot)) {
     message("No ScaleData slot found in @commands")
     stop()

R/Seurat.Utils.Visualization.R

@@ -3998,30 +3998,38 @@ panelCorPearson <- function(x, y, digits = 2, prefix = "", cex.cor = 2, method =
 suPlotVariableFeatures <- function(obj = combined.obj, NrVarGenes = 15,
                                    repel = TRUE, plotWidth = 7, plotHeight = 5, save = TRUE,
                                    # suffix = kpp("nVF", .getNrScaledFeatures(obj)),
+                                   assay = DefaultAssay(obj),
                                    suffix = NULL,
                                    ...) {
-  # Input validation
+  message(" > Running suPlotVariableFeatures()...")
+  message(length(Cells(obj)), " cells | assay: ", assay, " | NrVarGenes: ", NrVarGenes)
+
   stopifnot(
     is(obj, "Seurat"), is.function(ppp), is.logical(repel),
     is.numeric(plotWidth), is.numeric(plotHeight)
   )
 
   obj.name <- deparse(substitute(obj))
 
-  plot1 <- Seurat::VariableFeaturePlot(obj) +
+  cat("1", "\n")
+  # browser()
+  plot1 <- Seurat::VariableFeaturePlot(obj, assay = assay) +
     theme(panel.background = element_rect(fill = "white")) +
-    ggtitle(label = "Variable Genes", subtitle = kppws(obj.name, suffix))
-
+    labs(title = "Variable Genes",
+         subtitle = kppws(obj.name, suffix),
+         caption = paste("Assay:", assay, "|", idate()))
+  cat("2", "\n")
 
   # Assuming LabelPoints is defined elsewhere and available for use.
-  TopVarGenes <- VariableFeatures(obj)[1:NrVarGenes]
+  TopVarGenes <- VariableFeatures(obj, assay = assay)[1:NrVarGenes]
   labeledPlot <- LabelPoints(
     plot = plot1, points = TopVarGenes, repel = repel,
     xnudge = 0, ynudge = 0, max.overlaps = 15
   )
+  cat("3", "\n")
   print(labeledPlot)
   filename <- ppp("Var.genes", obj.name, suffix, idate(), "png")
-
+  cat("4", "\n")
   # if (save) ggplot2::ggsave(plot = labeledPlot, filename = filename, width = plotWidth, height = plotHeight)
   if (save) {
     qqSave(