Fix LE DEG generation for Pd analysis

.gitignore

@@ -10,3 +10,4 @@ WR/
 *~
 temp_png.png
 Rplots.pdf
+stress/*

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)