Fix MergeSubClusts to handle Lineage ? pops as St

r.scripts/sc_MergeSubClust.R

@@ -45,7 +45,7 @@ Epi.cell <- names(sc10x.Group@ident[sc10x.Group@ident=="Epi"])
 St.cell <- c(names(sc10x.Group@ident[sc10x.Group@ident=="St"]),names(sc10x.Group@ident[sc10x.Group@ident=="?"]))
 
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Epi.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$Epi.res",opt.episubclust$r,"[sc10x.Group@ident=='Epi']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='St']"))))
+sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=c(eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='St']"))),eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='?']")))))
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("SubClust.res",opt$r))
 postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Global.Merge.res.eps"))
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
@@ -56,7 +56,7 @@ dev.off()
 
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Epi.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$Epi.sub.",opt$e,"[sc10x.Group@ident=='Epi']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='St']"))))
+sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=c(eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='St']"))),eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='?']")))))
 sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c(
   unique(as.character(sc10x.Group@ident)[grep("^Epi",as.character(sc10x.Group@ident))]),
   unique(as.character(sc10x.Group@ident)[grep("^BE",as.character(sc10x.Group@ident))]),