From 5af3d377a2b9158e26df15a75d5c26b5daa46b61 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 2 Nov 2018 15:00:09 -0500
Subject: [PATCH] Fix LE DEG generation for Pd analysis
---
.gitignore | 1 +
r.scripts/sc-TissueMapper_RUN.Pd.R | 4 +++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/.gitignore b/.gitignore
index 74eacbf..fa9ab1f 100755
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ WR/
*~
temp_png.png
Rplots.pdf
+stress/*
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index 7772609..cda01c1 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -11,6 +11,8 @@ library(monocle)
library(dplyr)
library(viridis)
+options(bitmapType="cairo")
+
source("../r.scripts/sc-TissueMapper.R")
#Create folder structure
@@ -411,7 +413,7 @@ genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2)
genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2)
genes.deg.BE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="BE",g.2=c("LE","OE1","OE2"),pct=0.25,t=2)
-genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
+genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","OE1","OE2"),pct=0.25,t=2)
genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE1",g.2=c("BE","LE","OE2"),pct=0.25,t=2)
genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE2",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
--
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