sc_DEG: change cairo to quartz in heatmaps, remove antialiassing from...

sc_DEG: change cairo to quartz in heatmaps, remove antialiassing from violin/ridge plots, select unique DEGs for pops and plot aggregated dot plot and save as .txt, save all DEGs in .Rda

r.scripts/sc_DEG.R

@@ -104,9 +104,24 @@ png(paste0("./analysis/",opt$g,"/global/DEG/Ridge.DEG.Stress.png"),1000,1000,poi
 plot(RidgePlot(sc10x.Group.Stress,features.plot=row.names(DEG.Stress)[1:10],nCol=5))
 dev.off()
 
+DEG.BE <- setdiff(rownames(DEG.BE.vs.Epi),Reduce(union,list(rownames(DEG.LE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.SM2.vs.SM1),rownames(DEG.Endo.vs.SM))))
+DEG.LE <- setdiff(rownames(DEG.LE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.SM2.vs.SM1),rownames(DEG.Endo.vs.SM))))
+DEG.OE <- setdiff(rownames(DEG.OE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.SM2.vs.SM1),rownames(DEG.Endo.vs.SM))))
+DEG.NE <- setdiff(rownames(DEG.NE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.SM2.vs.SM1),rownames(DEG.Endo.vs.SM))))
+DEG.SM1 <- setdiff(rownames(DEG.SM1.vs.SM2),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM2.vs.SM1),rownames(DEG.Endo.vs.SM))))
+DEG.SM2 <- setdiff(rownames(DEG.SM2.vs.SM1),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.Endo.vs.SM))))
+DEG.Endo <- setdiff(rownames(DEG.Endo.vs.SM),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM1.vs.SM2),rownames(DEG.SM2.vs.SM1))))
+DEG <- c(DEG.BE[1:10],DEG.LE[1:10],DEG.OE[1:10],DEG.NE[1:10],DEG.SM1[1:10],DEG.SM2[1:10],DEG.Endo[1:10])
+DEG <- rev(DEG)
+sc10x.Group.NoStress@ident <- factor(sc10x.Group.NoStress@ident,levels=rev(c("BE","LE","OE","NE","SM1","SM2","Endo")))
+png(paste0("./analysis/",opt$g,"/global/DEG/Dot.DEG.png"),1000,1000,pointsize=20,type="quartz",antialias="none",family="Arial")
+DotPlot(sc10x.Group.NoStress,DEG,x.lab.rot=TRUE,plot.legend=TRUE)
+dev.off()
+rm(DEG)
+
 for (i in ls(pattern="^DEG")){
   write.table(get(i),file=paste0("./analysis/",opt$g,"/global/DEG/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 }
 
 cat(row.names(DEG.Stress),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scStress.txt"),sep="\n")
-cat(row.names(DEG.NE.vs.Epi),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scNE.txt"),sep="\n")
+cat(row.names(DEG.NE.vs.Epi),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scNE.txt"),sep="\n")
\ No newline at end of file