From f2285a20f343821a85ade8c33ede45b70be18e29 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 27 Mar 2018 18:29:55 -0500
Subject: [PATCH] Add no downsampling (NA) as an option for sc_PC.Score.NE.R
---
r.scripts/sc_PC.Score.NE.R | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 42e3196..b9b5ef1 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -105,7 +105,11 @@ plot(plot)
dev.off()
#subsample all cells (+NE) to better visualize their clustering
-rnd <- sample(1:ncol(sc10x.Group@data),opt$sv)
+if (!is.na(opt$s)){
+ rnd <- sample(1:ncol(sc10x.Group@data),opt$sv)
+} else {
+ rnd <- 1:ncol(sc10x.Group@data)
+}
sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=sc10x.Group@data@Dimnames[[2]][rnd],ident.use="sample")
if (clust$size[1]<clust$size[2]){
clusterCut <- names(clusterCut[clusterCut==1])
--
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