Prevent error if anchor gene does not exist in data, PC.Score.Stress/NE.R

r.scripts/sc_PC.Score.NE.R

@@ -136,12 +136,13 @@ sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("NE","Epi","St"))
 #generate violin plot of NE gene expression
 anchors <- c("CHGA","CHGB","SYP")
 for (i in anchors){
-  postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/Violin_NE.",i,".eps"))
-  plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,point.size.use=2.5,size.title.use=25,x.lab.rot=TRUE)
-  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
-  plot(plot)
-  dev.off()
-}
+  if (i %in% rownames(sc10x.Group.sample@data)){
+    postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/Violin_NE.",i,".eps"))
+    plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,point.size.use=2.5,size.title.use=25,x.lab.rot=TRUE)
+    plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
+    plot(plot)
+    dev.off()
+}}
 rm(anchors)
 
 #save NE identity

r.scripts/sc_PC.Score.Stress.R

@@ -114,12 +114,13 @@ sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=clusterCut,ident.use="Stres
 #generate violin plot of stres gene expression
 anchors <- c("EGR1","FOS","JUN")
 for (i in anchors){
-  postscript(paste0("./analysis/",opt$g,"/pc-score/Violin_Stress.",i,".eps"))
-  plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,point.size.use=2.5,size.title.use=25,x.lab.rot=TRUE)
-  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
-  plot(plot)
-  dev.off()
-}
+  if (i %in% rownames(sc10x.Group@data)){
+    postscript(paste0("./analysis/",opt$g,"/pc-score/Violin_Stress.",i,".eps"))
+    plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,point.size.use=2.5,size.title.use=25,x.lab.rot=TRUE)
+    plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
+    plot(plot)
+    dev.off()
+}}
 rm(anchors)
 
 #save stress cell identity