Add Lineage UK cells to St for analysis

r.scripts/sc_LineageSubClust.R

@@ -47,25 +47,18 @@ if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
 sc10x.Group.Epi <- SubsetData(object=sc10x.Group,ident.use="Epi")
 sc10x.Group.St <- SubsetData(object=sc10x.Group,ident.use="St")
-UK <- TRUE
 tryCatch({
-  sc10x.Group.UK <- SubsetData(object=sc10x.Group,ident.use="?")
-},error=function(e){UK <<- FALSE})
+  sc10x.Group.St <- SubsetData(object=sc10x.Group,ident.use=c("St","?"))
+},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
 rm(sc10x.Group)
 
 #re-detect variable genes in Epi + St subsets
 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)
-if (UK==TRUE){
-  sc10x.Group.UK <- FindVariableGenes(object=sc10x.Group.UK,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.0125,x.high.cutoff=3,y.cutoff=0.5,do.plot=FALSE)
-}
 
 #re-PCA on new variable genes
 sc10x.Group.Epi <- RunPCA(object=sc10x.Group.Epi,pc.genes=sc10x.Group.Epi@var.genes,do.print=FALSE,pcs.compute=50)
 sc10x.Group.St <- RunPCA(object=sc10x.Group.St,pc.genes=sc10x.Group.St@var.genes,do.print=FALSE,pcs.compute=50)
-if (UK==TRUE){
-  sc10x.Group.UK <- RunPCA(object=sc10x.Group.UK,pc.genes=sc10x.Group.St@var.genes,do.print=FALSE,pcs.compute=50)
-}
 
 #generate QC figures
 postscript(paste0("./analysis/",opt$g,"/qc/Plot_PCElbow.Epi.eps"))
@@ -80,14 +73,6 @@ plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(si
 plot(plot)
 dev.off()
 
-if (UK==TRUE){
-  postscript(paste0("./analysis/",opt$g,"/qc/Plot_PCElbow.UK.eps"))
-  plot <- PCElbowPlot(object=sc10x.Group.UK,num.pc=50)
-  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
-  plot(plot)
-  dev.off()
-}
-
 #re-generate tSNE dimensions and generage sample figures
 sc10x.Group.Epi <- RunTSNE(object=sc10x.Group.Epi,dims.use=1:PC.Max,do.fast=TRUE)
 postscript(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Sample.Epi.eps"))
@@ -105,29 +90,13 @@ plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
 plot(plot)
 dev.off()
 
-if (UK==TRUE){
-  sc10x.Group.UK <- RunTSNE(object=sc10x.Group.UK,dims.use=1:PC.Max,do.fast=TRUE)
-  postscript(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Sample.UK.eps"))
-  plot <- TSNEPlot(object=sc10x.Group.UK,group.by="samples",pt.size=2.5,do.return=TRUE)
-  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
-  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
-  plot(plot)
-  dev.off()
-}
-
 #re-cluster at different resolutions and generate figures
-if (UK==TRUE){
-  pops <- c("Epi","St","UK")
-} else {
-  pops <- c("Epi","St")
-}
+pops <- c("Epi","St")
 for (j in pops){
   if (j=="Epi"){
     sc10x.Group <- sc10x.Group.Epi
   } else if (j=="St") {
     sc10x.Group <- sc10x.Group.St
-  } else if (j=="UK") {
-    sc10x.Group <- sc10x.Group.UK
   }
   for (i  in c(5,2,1,0.5,0.2,0.1)){
     gc()  
@@ -145,8 +114,6 @@ for (j in pops){
     sc10x.Group.Epi <- sc10x.Group
   } else if (j=="St"){
     sc10x.Group.St <- sc10x.Group
-  } else {
-    sc10x.Group.UK <- sc10x.Group
 }}
 rm(pops)
 rm(sc10x.Group)
@@ -162,13 +129,8 @@ rm(opt)
 #save subcluster .Rda files
 save(sc10x.Group.Epi,file=paste0("./analysis/sc10x.",Project.Name,".",opt.subclust$g,".EpiSubcluster",sub.file,".Rda"))
 save(sc10x.Group.St,file=paste0("./analysis/sc10x.",Project.Name,".",opt.subclust$g,".StSubcluster",sub.file,".Rda"))
-if (UK==TRUE){
-  save(sc10x.Group.UK,file=paste0("./analysis/sc10x.",Project.Name,".",opt.subclust$g,".UKSubcluster",sub.file,".Rda"))
-}
-rm(UK)
 rm(sc10x.Group.Epi)
 rm(sc10x.Group.St)
-rm(sc10x.Group.UK)
 rm(sub.folder)
 rm(sub.file)
 save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))

r.scripts/sc_MergeSubClust.R

@@ -43,12 +43,10 @@ if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
 #merge Epi and St SubClust and generate tSNEs
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
 Epi.cell <- names(sc10x.Group@ident[sc10x.Group@ident=="Epi"])
-St.cell <- names(sc10x.Group@ident[sc10x.Group@ident=="St"])
-UK.cell <- names(sc10x.Group@ident[sc10x.Group@ident=="?"])
+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$Epi.res",opt$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$St.res",opt$r,"[sc10x.Group@ident=='St']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=UK.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$UK.res",opt$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",opt$r,".eps"))
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
@@ -60,7 +58,6 @@ dev.off()
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Epi.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$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$s,"[sc10x.Group@ident=='St']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=UK.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$UK.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))]),
@@ -90,7 +87,6 @@ dev.off()
 rm(plot)
 rm(Epi.cell)
 rm(St.cell)
-rm(UK.cell)
 
 #make generic variables of run specific variables
 Group.List <- c(Group.List,paste0("SubClust.res",opt$r),"SubClust.ID")