Fix sc_LineageSubClust.R

r.scripts/sc_LineageSubClust.R

@@ -49,7 +49,7 @@ sc10x.Group.Epi <- SubsetData(object=sc10x.Group,ident.use="Epi")
 sc10x.Group.St <- SubsetData(object=sc10x.Group,ident.use="St")
 tryCatch({
   sc10x.Group.UK <- SubsetData(object=sc10x.Group,ident.use="?")
-},error={UK <- FALSE})
+},error=function(e){UK <<- FALSE})
 rm(sc10x.Group)
 
 #re-detect variable genes in Epi + St subsets
@@ -78,6 +78,7 @@ plot <- PCElbowPlot(object=sc10x.Group.St,num.pc=50)
 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 (UK==TRUE){
   postscript(paste0("./analysis/",opt$g,"/qc/Plot_PCElbow.UK.eps"))
   plot <- PCElbowPlot(object=sc10x.Group.UK,num.pc=50)
@@ -113,11 +114,11 @@ if (UK==TRUE){
   dev.off()
 }
 
-re-cluster at different resolutions and generate figures
+#re-cluster at different resolutions and generate figures
 if (UK==TRUE){
-  pops <- c("Epi","St","UK"){
+  pops <- c("Epi","St","UK")
 } else {
-    pops <- c("Epi","St"){
+  pops <- c("Epi","St")
 }
 for (j in pops){
   if (j=="Epi"){
@@ -145,8 +146,7 @@ for (j in pops){
     sc10x.Group.St <- sc10x.Group
   } else {
     sc10x.Group.UK <- sc10x.Group
-  }
-}
+}}
 rm(pops)
 rm(sc10x.Group)
 rm(plot)
@@ -154,7 +154,6 @@ rm(i)
 rm(j)
 
 #make generic variables of run specific variables
-rm(UK)
 rm(PC.Max)
 opt.subclust <- opt
 rm(opt)
@@ -165,6 +164,7 @@ save(sc10x.Group.St,file=paste0("./analysis/sc10x.",Project.Name,".",opt.subclus
 if (UK==TRUE){
   save(sc10x.Group.UK,file=paste0("./analysis/sc10x.",Project.Name,".",opt.subclust$g,".UKSubcluster",sub.file,".Rda"))
 }
+rm(UK)
 rm(sc10x.Group.Epi)
 rm(sc10x.Group.St)
 rm(sc10x.Group.UK)