Finalize test code for lineage sub-clustering *still needs to be cleaned up before merging*

r.scripts/sc_LineageSubClust.R

@@ -33,6 +33,16 @@ sc10x.Group.Epi <- SubsetData(object=sc10x.Group,ident.use="Epi")
 sc10x.Group.St <- SubsetData(object=sc10x.Group,ident.use="St")
 sc10x.Group.All <- sc10x.Group
 
+if (!dir.exists(paste0("./anaysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
+}
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
+}
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder))
+}
+
 sc10x.Group.Epi <- FindVariableGenes(object=sc10x.Group.Epi,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.0125,x.high.cutoff=3,y.cutoff=0.5,do.plot=FALSE)
 sc10x.Group.St <- FindVariableGenes(object=sc10x.Group.St,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.0125,x.high.cutoff=3,y.cutoff=0.5,do.plot=FALSE)
 
@@ -84,4 +94,13 @@ for (j in (c("Epi","St"))){
     plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
     plot(plot)
     dev.off()
-}}
\ No newline at end of file
+  }
+  if (j=="Epi"){
+    sc10x.Group.Epi <- sc10x.Group
+  } else {
+    sc10x.Group.St <- sc10x.Group
+  }
+}
+
+save(sc10x.Group.Epi,file=paste0("./analysis/sc10x.",Project.Name,".",opt.lgeaepipop$g,".EpiSubcluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
+save(sc10x.Group.St,file=paste0("./analysis/sc10x.",Project.Name,".",opt.lgeaepipop$g,".StSubcluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
\ No newline at end of file