From cbe5d3faef72d7b83efd3e9e4fa948a8bd78d02d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 20 May 2018 19:46:38 -0500
Subject: [PATCH] When use DWS NE geneset, use 100 bins (instead of 50) for
NE-Score (PC1) turning point choice
---
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 bf657dc..a6c5e00 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -89,7 +89,11 @@ dev.off()
#find first turning point on a KDE of NE1
#hist(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=1),prob=TRUE)
-d1 <- density(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=1),n=50)
+if (opt$u==FALSE){
+ d1 <- density(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=1),n=50)
+} else {
+ d1 <- density(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=1),n=100)
+}
#d2 <- density(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=2))
#lines(d1,col="blue")
ts_1 <- ts(d1$y)
--
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