From 6a0e0cb80c742ab83761cadabd81ea83eb864468 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 14 May 2018 12:37:38 -0500
Subject: [PATCH] Change find cutoff in PCA for Stress and NE to first local
minima after global maxima
---
r.scripts/sc_PC.Score.NE.R | 2 +-
r.scripts/sc_PC.Score.Stress.R | 5 ++++-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index fa09ed9..9acccfa 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -96,7 +96,7 @@ ts_1 <- ts(d1$y)
#ts_2 <- ts(d2$y)
tp1 <- turnpoints(ts_1)
#tp2 <- turnpoints(ts_2)
-pit1 <- min(d1$x[tp1$pits][d1$y[tp1$pits]==min(d1$y[tp1$pits])])
+pit1 <- min(d1$x[tp1$pits][d1$x[tp1$pits]>d1$x[tp1$peaks][d1$y[tp1$peaks]==max(d1$y[tp1$peaks])]])
#pit2 <- d2$x[tp2$pits][length(d2$x[tp2$pits])]
#abline(v=pit1)
diff --git a/r.scripts/sc_PC.Score.Stress.R b/r.scripts/sc_PC.Score.Stress.R
index 7ee2ac5..176d89b 100755
--- a/r.scripts/sc_PC.Score.Stress.R
+++ b/r.scripts/sc_PC.Score.Stress.R
@@ -75,13 +75,14 @@ plot(plot)
dev.off()
#find first turning point on a KDE of Stress1
+histo <- hist(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=1),breaks=10,prob=TRUE,plot=TRUE)
d1 <- density(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=1),n=1000)
#d2 <- density(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=2),n=1000)
ts_1 <- ts(d1$y)
#ts_2 <- ts(d2$y)
tp1 <- turnpoints(ts_1)
#tp2 <- turnpoints(ts_2)
-pit1 <- min(d1$x[tp1$pits])
+pit1 <- min(d1$x[tp1$pits][d1$x[tp1$pits]>d1$x[tp1$peaks][d1$y[tp1$peaks]==max(d1$y[tp1$peaks])]])
#pit2 <- min(d2$x[tp2$pits])
#plot clusters
@@ -98,6 +99,8 @@ plot <- plot+geom_vline(xintercept=pit1,color="red",lwd=2.5)
plot(plot)
dev.off()
+
+
#subsample all cells (+Stress) to better visualize their clustering
if (!is.na(opt$s)){
rnd <- sample(1:ncol(sc10x.Group@data),opt$sv)
--
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