From 0affc7367be5a7fe007dbd08038cdc6bbf86514b Mon Sep 17 00:00:00 2001
From: vertesy <abel.vertesy@imba.oeaw.ac.at>
Date: Wed, 4 Dec 2024 17:54:05 +0100
Subject: [PATCH] nf Convert10Xfolders NormalizeData

---
 R/Seurat.Utils.Metadata.R | 10 +++++-----
 R/Seurat.Utils.R          |  5 +++++
 man/Convert10Xfolders.Rd  |  3 +++
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/R/Seurat.Utils.Metadata.R b/R/Seurat.Utils.Metadata.R
index 147dd74..a537ec3 100644
--- a/R/Seurat.Utils.Metadata.R
+++ b/R/Seurat.Utils.Metadata.R
@@ -526,6 +526,11 @@ addMetaFraction <- function(
     layer = "data",
     gene.set = FALSE,
     verbose = TRUE) {
+  #
+  message("Should rather use the default `Seurat::PercentageFeatureSet`")
+  message("Assay: ", assay)
+  message("Layer: ", layer)
+
   stopifnot(
     is(obj, "Seurat"),
     is.character(col.name), is.character(assay), is.character(layer),
@@ -533,11 +538,6 @@ addMetaFraction <- function(
     assay %in% Assays(obj), layer %in% Layers(obj)
   )
 
-  message("Should rather use the default `Seurat::PercentageFeatureSet`")
-  message("Assay: ", assay)
-  message("Layer: ", layer)
-
-
   stopif(condition = isFALSE(gene.set) && isFALSE(gene.symbol.pattern), "Either gene.set OR gene.symbol.pattern has to be defined (!= FALSE).")
   if (!isFALSE(gene.set) && !isFALSE(gene.symbol.pattern) && verbose) print("Both gene.set AND gene.symbol.pattern are defined. Only using gene.set.")
 
diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R
index 17ee1ba..25fe55d 100644
--- a/R/Seurat.Utils.R
+++ b/R/Seurat.Utils.R
@@ -4421,6 +4421,7 @@ PlotUpdateStats <- function(mat = UpdateStatMat, column.names = c("Updated (%)",
 #' @param suffix A character string specifying the suffix of the files saved.
 #' @param min.cells An integer value specifying the minimum number of cells. Default: 5.
 #' @param min.features An integer value specifying the minimum number of features. Default: 200.
+#' @param normalize_data Add normalized "data" layer?. Default: `TRUE`.
 #' @param updateHGNC A logical value indicating whether to update the HGNC. Default: `TRUE`.
 #' @param save Save .qs object? Default: `TRUE`.
 #' @param ShowStats A logical value indicating whether to show statistics. Default: `TRUE`.
@@ -4441,6 +4442,7 @@ Convert10Xfolders <- function(
     suffix = strsplit(folderPattern, "_")[[1]][1],
     depth = 4,
     min.cells = 5, min.features = 200,
+    normalize_data = TRUE,
     updateHGNC = TRUE, ShowStats = TRUE,
     writeCBCtable = TRUE,
     nthreads = .getNrCores(),
@@ -4499,6 +4501,9 @@ Convert10Xfolders <- function(
     # update --- --- ---
     if (updateHGNC) seu <- UpdateGenesSeurat(seu, EnforceUnique = TRUE, ShowStats = TRUE)
 
+    # NormalizeData --- --- ---
+    if (normalize_data) seu <- NormalizeData(seu, normalization.method = "LogNormalize", scale.factor = 10000,  verbose = TRUE)
+
     # write out --- --- ---
     if (save) qs::qsave(x = seu, file = f.path.out, nthreads = nthreads, preset = preset)
 
diff --git a/man/Convert10Xfolders.Rd b/man/Convert10Xfolders.Rd
index a5f01f0..b922633 100644
--- a/man/Convert10Xfolders.Rd
+++ b/man/Convert10Xfolders.Rd
@@ -12,6 +12,7 @@ Convert10Xfolders(
   depth = 4,
   min.cells = 5,
   min.features = 200,
+  normalize_data = TRUE,
   updateHGNC = TRUE,
   ShowStats = TRUE,
   writeCBCtable = TRUE,
@@ -38,6 +39,8 @@ Convert10Xfolders(
 
 \item{min.features}{An integer value specifying the minimum number of features. Default: 200.}
 
+\item{normalize_data}{Add normalized "data" layer?. Default: \code{TRUE}.}
+
 \item{updateHGNC}{A logical value indicating whether to update the HGNC. Default: \code{TRUE}.}
 
 \item{ShowStats}{A logical value indicating whether to show statistics. Default: \code{TRUE}.}