diff --git a/bash.scripts/sc_TissueMapper-PdPbPc.sh b/bash.scripts/sc_TissueMapper-PdPbPc.sh
index 7422a5c2e571b2a565245d3b48b766f68672690c..3cbf55f5bf89c96ea43c666b202d27bb2dd61e9e 100644
--- a/bash.scripts/sc_TissueMapper-PdPbPc.sh
+++ b/bash.scripts/sc_TissueMapper-PdPbPc.sh
@@ -8,7 +8,11 @@
 #SBATCH --mail-type ALL
 #SBATCH --mail-user gervaise.henry@utsouthwestern.edu
 
-module load R/3.4.1-gccmkl
+sh sc_LinkData.sh Pd Pd
+sh sc_LinkData.sh Pb Pb
+sh sc_LinkData.sh Pc Pc
+
+module load R/3.4.1-gccmkl_20181025
 
 Rscript ../r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R &
 Rscript ../r.scripts/sc-TissueMapper_RUN.PdPbPc.Pb.R &
diff --git a/r.scripts/sc-TissueMapper_RUN.PdPbPc.R b/r.scripts/sc-TissueMapper_RUN.PdPbPc.R
index 24eeb91a0a54e00bd2cfcc4e8b5edf1df1cd2288..aeb3cfbbfa218f5154801c3387c886828eff3acb 100755
--- a/r.scripts/sc-TissueMapper_RUN.PdPbPc.R
+++ b/r.scripts/sc-TissueMapper_RUN.PdPbPc.R
@@ -58,12 +58,18 @@ if (!dir.exists("./analysis/tSNE/lin")){
 if (!dir.exists("./analysis/tSNE/epi")){
   dir.create("./analysis/tSNE/epi")
 }
+if (!dir.exists("./analysis/tSNE/n-epi")){
+  dir.create("./analysis/tSNE/n-epi")
+}
 if (!dir.exists("./analysis/tSNE/st")){
   dir.create("./analysis/tSNE/st")
 }
 if (!dir.exists("./analysis/tSNE/leu")){
   dir.create("./analysis/tSNE/leu")
 }
+if (!dir.exists("./analysis/tSNE/t")){
+  dir.create("./analysis/tSNE/t")
+}
 if (!dir.exists("./analysis/tSNE/merge")){
   dir.create("./analysis/tSNE/merge")
 }
@@ -126,21 +132,27 @@ for (i in c("Pb","Pc","Pd")){
   if (!dir.exists(paste0("./analysis/tSNE/post.stress/",i))){
     dir.create(paste0("./analysis/tSNE/post.stress/",i))
   }
-    if (!dir.exists(paste0("./analysis/tSNE/lin/",i))){
+  if (!dir.exists(paste0("./analysis/tSNE/lin/",i))){
     dir.create(paste0("./analysis/tSNE/lin/",i))
   }
   if (!dir.exists(paste0("./analysis/tSNE/epi/",i))){
     dir.create(paste0("./analysis/tSNE/epi/",i))
   }
+  if (!dir.exists(paste0("./analysis/tSNE/n-epi/",i))){
+    dir.create(paste0("./analysis/tSNE/n-epi/",i))
+  }
   if (!dir.exists(paste0("./analysis/tSNE/st/",i))){
     dir.create(paste0("./analysis/tSNE/st/",i))
   }
   if (!dir.exists(paste0("./analysis/tSNE/leu/",i))){
     dir.create(paste0("./analysis/tSNE/leu/",i))
   }
-
+  if (!dir.exists(paste0("./analysis/tSNE/t/",i))){
+    dir.create(paste0("./analysis/tSNE/t/",i))
+  }
+  
   sc10x <- get(paste0("sc10x.",i))
-    
+  
   sc10x <- scCluster(sc10x,pc.use=opt$acca,res.use=opt$res.poststress,folder=paste0("post.stress/",i),red="cca.aligned")
   
   gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
@@ -153,8 +165,8 @@ for (i in c("Pb","Pc","Pd")){
   gene.set <- c(gene.set,gene.set1)
   rm(gene.set1)
   gc()
-  min.all <- min(table(sc10x@meta.data[,paste0("res",0.5)]))
-  results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Lin",folder=paste0("lin/",i))
+  min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
+  results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder=paste0("lin/",i))
   sc10x <- results[[1]]
   results.cor.Lin <- results[[2]]
   results.clust.Lin.id <- results[[3]]
@@ -164,15 +176,12 @@ for (i in c("Pb","Pc","Pd")){
   sc10x <- SetAllIdent(object=sc10x,id="Lin")
   sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
   if (any(levels(sc10x@ident)=="Unknown")){
-    sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
+    sc10x.nEpi <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
   } else {
-    sc10x.St <- scSubset(sc10x,i="Lin",g="St")
+    sc10x.nEpi <- scSubset(sc10x,i="Lin",g="St")
   }
   
   sc10x.Epi <- scCluster(sc10x.Epi,pc.use=opt$acca,res.use=opt$res.poststress,folder=paste0("epi/",i),red="cca.aligned")
-  
-  #sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
-  #sc10x.Epi <- BuildClusterTree(sc10x.Epi,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
   sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name=paste0("res",opt$res.poststress))
   
   sc10x.Epi <- RunTSNE(object=sc10x.Epi,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
@@ -213,29 +222,25 @@ for (i in c("Pb","Pc","Pd")){
   rm(gene.set1)
   gc()
   min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
-  results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Epi.dws.sc",folder=paste0("epi/",i))
+  results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws.sc",folder=paste0("epi/",i))
   sc10x.Epi <- results[[1]]
   results.cor.Epi <- results[[2]]
   results.clust.Epi.id <- results[[3]]
   rm(results)
   rm(gene.set)
   
+  sc10x.nEpi <- scCluster(sc10x.nEpi,pc.use=opt$acca,res.use=opt$res.poststress,folder=paste0("n-epi/",i),red="cca.aligned")
+  sc10x.nEpi <- StashIdent(object=sc10x.nEpi,save.name=paste0("res",opt$res.poststress))
   
-  sc10x.St <- scCluster(sc10x.St,pc.use=opt$acca,res.use=opt$res.poststress,folder=paste0("st/",i),red="cca.aligned")
-  
-  #sc10x.St <- SetAllIdent(object=sc10x.St,id=paste0("res",opt$res.poststress))
-  #sc10x.St <- BuildClusterTree(sc10x.St,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
-  sc10x.St <- StashIdent(object=sc10x.St,save.name=paste0("res",opt$res.poststress))
-  
-  sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
-  postscript(paste0("./analysis/tSNE/st/",i,"/tSNE_Sample.eps"))
-  plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+  sc10x.nEpi <- RunTSNE(object=sc10x.nEpi,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
+  postscript(paste0("./analysis/tSNE/n-epi/",i,"/tSNE_Sample.eps"))
+  plot <- TSNEPlot(object=sc10x.nEpi,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
   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()
-  postscript(paste0("./analysis/tSNE/st/",i,"/tSNE_res",opt$res.poststress,".eps"))
-  plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+  postscript(paste0("./analysis/tSNE/n-epi/",i,"/tSNE_res",opt$res.poststress,".eps"))
+  plot <- TSNEPlot(object=sc10x.nEpi,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
   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)
@@ -257,29 +262,39 @@ for (i in c("Pb","Pc","Pd")){
   gene.set1 <- as.list(gene.set1)
   names(gene.set1) <- "Fib"
   gene.set <- c(gene.set,gene.set1)
-  
-  genes.leu <- read_excel("genesets/40425_2017_215_MOESM1_ESM.xlsx",sheet="S3. Candidate markers")
-  leu <- as.list(unique(genes.leu[,2]))$Cell
-  leu <- leu[-c(1,3,4,7:9,14,15,17:18,20:21,23:30)]
-  genes.leu <- genes.leu[genes.leu$Selected==1,]
-  genes.leu <- genes.leu[unlist(genes.leu[,2]) %in% unlist(leu),]
-  gene.set1 <- split(genes.leu[,1], genes.leu[,2])
-  gene.set1 <- lapply(gene.set1,unname)
-  gene.set1 <- lapply(gene.set1,unlist)
-  gene.set <- c(gene.set,gene.set1)
-  
   rm(gene.set1)
   gc()
-  min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
-  results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="St.dws.sc",folder=paste0("st/",i))
-  sc10x.St <- results[[1]]
+  min.nepi <- min(table(sc10x.nEpi@meta.data[,paste0("res",opt$res.poststress)]))
+  results <- scQuSAGE(sc10x.nEpi,gs=gene.set,res.use=opt$res.poststress,ds=min.nepi,nm="St.dws.sc",folder=paste0("n-epi/",i))
+  sc10x.nEpi <- results[[1]]
   results.cor.St <- results[[2]]
   results.clust.St.id <- results[[3]]
   rm(results)
   rm(gene.set)
   
-  sc10x.St <- SetAllIdent(object=sc10x.St,id="St.dws.sc")
-  sc10x.Leu <- scSubset(sc10x.St,i="St.dws.sc",g=leu[leu %in% unique(sc10x.St@ident)])
+  sc10x.nEpi <- SetAllIdent(object=sc10x.nEpi,id="St.dws.sc")
+  sc10x.St <- scSubset(sc10x.nEpi,i="St.dws.sc",g=c("Fib","SM","Endo")[c("Fib","SM","Endo") %in% unique(sc10x.nEpi@ident)])
+  sc10x.Leu <- scSubset(sc10x.nEpi,i="St.dws.sc",g="Unknown")
+  
+  sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
+  postscript(paste0("./analysis/tSNE/st/",i,"/tSNE_Sample.eps"))
+  plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+  plot(plot)
+  dev.off()
+  postscript(paste0("./analysis/tSNE/st/",i,"/tSNE_St.dws.sc.eps"))
+  plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+  plot(plot)
+  dev.off()
+  rm(plot)
+  
+  opt$res.leu <- 2
+  
+  sc10x.Leu <- scCluster(sc10x.Leu,pc.use=opt$acca,res.use=opt$res.leu,folder=paste0("leu/",i),red="cca.aligned")
+  sc10x.Leu <- StashIdent(object=sc10x.Leu,save.name=paste0("res",opt$res.leu))
   
   sc10x.Leu <- RunTSNE(object=sc10x.Leu,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
   postscript(paste0("./analysis/tSNE/leu/",i,"/tSNE_Sample.eps"))
@@ -288,7 +303,7 @@ for (i in c("Pb","Pc","Pd")){
   plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
   plot(plot)
   dev.off()
-  postscript(paste0("./analysis/tSNE/leu/",i,"/tSNE_LeuLin.eps"))
+  postscript(paste0("./analysis/tSNE/leu/",i,"/tSNE_res",opt$res.leu,".eps"))
   plot <- TSNEPlot(object=sc10x.Leu,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
   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)))
@@ -296,43 +311,142 @@ for (i in c("Pb","Pc","Pd")){
   dev.off()
   rm(plot)
   
-  sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Epi.dws.sc",i.2="St.dws.sc",nm="Merge")
+  genes.leu <- read_excel("genesets/40425_2017_215_MOESM1_ESM.xlsx",sheet="S3. Candidate markers")
+  leu <- as.list(unique(genes.leu[,2]))$Cell
+  leu.l <- leu[-c(1,3,4,7:9,14,15,17:18,20:21,23:30)]
+  leu.t <- leu[-c(1,2,5,6,8:13,17:20,22)]
+#  genes.leu.s <- genes.leu[genes.leu$Selected==1,]
+#  leu.s <- as.list(unique(genes.leu.s[,2]))$Cell
+  genes.leu <- genes.leu[unlist(genes.leu[,2]) %in% unlist(leu),]
+  genes.leu.l <- genes.leu[unlist(genes.leu[,2]) %in% unlist(leu.l),]
+#  genes.leu.s <- genes.leu.s[unlist(genes.leu.s[,2]) %in% unlist(leu),]
+genes.leu.t <- genes.leu[unlist(genes.leu[,2]) %in% unlist(leu.t),]
   
-  sc10x@ident <- factor(sc10x@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
-  sctSNE3CustCol(sc10x,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=i)
-
-  if (i=="Pd"){
-    for (j in list(c("D17PrPzF_Via","D27PrPzF_Via","D35PrPzF_Via"),c("D17PrTzF_Via","D27PrTzF_Via","D35PrTzF_Via"))){
-      sc10x.sub <- scSubset(sc10x,"samples",j)
-      sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
-      sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
-      sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".",substr(j[1],6,7)))
-    }
-  rm(sc10x.sub)
-  } else if (i=="Pb"){
-    sc10x.sub <- scSubset(sc10x,"Glandular","Glandular")
-    sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
-    sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
-    sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".Glandular"))
-    
-    sc10x.sub <- scSubset(sc10x,"Stromal","Stromal")
-    sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
-    sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
-    sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".Stromal"))
+#   gene.set1 <- split(genes.leu[,1], genes.leu[,2])
+#   gene.set1 <- lapply(gene.set1,unname)
+#   gene.set1 <- lapply(gene.set1,unlist)
+#   gene.set <- gene.set1
+#   rm(gene.set1)
+#   gc()
+#   min.leu <- min(table(sc10x.Leu@meta.data[,paste0("res",opt$res.leu)]))
+#   results <- scQuSAGE(sc10x.Leu,gs=gene.set,res.use=opt$res.leu,ds=0,nm="Leu",folder=paste0("leu/",i))
+#   sc10x.Leu <- results[[1]]
+#   results.cor.Leu <- results[[2]]
+#   results.clust.Leu.id <- results[[3]]
+#   rm(results)
+#   rm(gene.set)
+#   gene.set1 <- split(genes.leu.s[,1], genes.leu.s[,2])
+#   gene.set1 <- lapply(gene.set1,unname)
+#   gene.set1 <- lapply(gene.set1,unlist)
+#   gene.set <- gene.set1
+#   rm(gene.set1)
+#   gc()
+#   sc10x.Leu <- SetAllIdent(object=sc10x.Leu,id=paste0("res",opt$res.leu))
+#   results <- scQuSAGE(sc10x.Leu,gs=gene.set,res.use=opt$res.leu,ds=0,nm="Leu.s",folder=paste0("leu/",i))
+#   sc10x.Leu <- results[[1]]
+#   results.cor.Leu.s <- results[[2]]
+#   results.clust.Leu.s.id <- results[[3]]
+#   rm(results)
+#   rm(gene.set)
+  gene.set1 <- split(genes.leu.l[,1], genes.leu.l[,2])
+  gene.set1 <- lapply(gene.set1,unname)
+  gene.set1 <- lapply(gene.set1,unlist)
+  gene.set <- gene.set1
+  rm(gene.set1)
+  gc()
+  sc10x.Leu <- SetAllIdent(object=sc10x.Leu,id=paste0("res",opt$res.leu))
+  results <- scQuSAGE(sc10x.Leu,gs=gene.set,res.use=opt$res.leu,ds=0,nm="Leu.l",folder=paste0("leu/",i))
+  sc10x.Leu <- results[[1]]
+  results.cor.Leu.l <- results[[2]]
+  results.clust.Leu.l.id <- results[[3]]
+  rm(results)
+  rm(gene.set)
 
-    for (j in c("BPH327PrGF_Via","BPH327PrSF_Via")){
-      sc10x.sub <- scSubset(sc10x,"samples",j)
-      sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
-      sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
-      sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".",substr(j,4,6),substr(j,9,9)))
-    }
-  }
+  sc10x.T <- scSubset(sc10x.Leu,i="Leu.l",g="T-cells")
 
-  write.table(table(sc10x@meta.data[,"samples"],sc10x@meta.data[,"Merge"]),file=paste0("./analysis/table/Table_samples_Merge",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(round(prop.table(table(sc10x@meta.data[,"samples"],sc10x@meta.data[,"Merge"]),1)*100,1),file=paste0("./analysis/table/ProbTable_samples_Merge",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  sc10x.T <- scCluster(sc10x.T,pc.use=opt$acca,res.use=opt$res.leu,folder=paste0("t/",i),red="cca.aligned")
+  sc10x.T <- StashIdent(object=sc10x.T,save.name=paste0("res",opt$res.leu))
   
+  sc10x.T <- RunTSNE(object=sc10x.T,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
+  postscript(paste0("./analysis/tSNE/t/",i,"/tSNE_Sample.eps"))
+  plot <- TSNEPlot(object=sc10x.T,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+  plot(plot)
+  dev.off()
+  postscript(paste0("./analysis/tSNE/t/",i,"/tSNE_res",opt$res.leu,".eps"))
+  plot <- TSNEPlot(object=sc10x.T,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+  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()
+  rm(plot)
+
+  gene.set1 <- split(genes.leu.t[,1], genes.leu.t[,2])
+  gene.set1 <- lapply(gene.set1,unname)
+  gene.set1 <- lapply(gene.set1,unlist)
+  gene.set <- gene.set1
+  rm(gene.set1)
+  gc()
+  sc10x.T <- SetAllIdent(object=sc10x.T,id=paste0("res",opt$res.leu))
+  results <- scQuSAGE(sc10x.T,gs=gene.set,res.use=opt$res.leu,ds=0,nm="Leu.t",folder=paste0("t/",i))
+  sc10x.Leu <- results[[1]]
+  results.cor.Leu.l <- results[[2]]
+  results.clust.Leu.l.id <- results[[3]]
+  rm(results)
+  rm(gene.set)
+
+
+
+#   
+#   sc10x.Merge <- scMerge(sc10x.nEpi,sc10x.St,sc10x.Leu,i.1="St.dws.sc",i.2="Leu",nm="Merge")
+#   sc10x.Merge <- scMerge(sc10x,sc10x.Epi,sc10x.Merge,i.1="Epi.dws.sc",i.2="Merge",nm="Merge")
+#   
+#   sc10x.Merge@ident <- factor(sc10x.Merge@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo",leu))
+#   
+#   postscript(paste0("./analysis/tSNE/FINAL/tSNE_Merge_",i,".eps"))
+#   plot <- TSNEPlot(object=sc10x.Merge,pt.size=2.5,do.label=TRUE,label.size=5,do.return=TRUE,vector.friendly=FALSE)
+#   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()
+#   rm(plot)
+#   
+#   sctSNE3CustCol(sc10x,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=i)
+#   
+#   if (i=="Pd"){
+#     for (j in list(c("D17PrPzF_Via","D27PrPzF_Via","D35PrPzF_Via"),c("D17PrTzF_Via","D27PrTzF_Via","D35PrTzF_Via"))){
+#       sc10x.sub <- scSubset(sc10x,"samples",j)
+#       sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
+#       sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
+#       sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".",substr(j[1],6,7)))
+#     }
+#     rm(sc10x.sub)
+#   } else if (i=="Pb"){
+#     sc10x.sub <- scSubset(sc10x,"Glandular","Glandular")
+#     sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
+#     sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
+#     sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".Glandular"))
+#     
+#     sc10x.sub <- scSubset(sc10x,"Stromal","Stromal")
+#     sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
+#     sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
+#     sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".Stromal"))
+#     
+#     for (j in c("BPH327PrGF_Via","BPH327PrSF_Via")){
+#       sc10x.sub <- scSubset(sc10x,"samples",j)
+#       sc10x.sub <- SetAllIdent(object=sc10x.sub,id="Merge")
+#       sc10x.sub@ident <- factor(sc10x.sub@ident,levels=c("BE","LE","Hillock","Club","Fib","SM","Endo","B-cells","T-cells","Macrophages","Mast cells"))
+#       sctSNE3CustCol(sc10x.sub,i="Merge",bl=c("BE","LE","Hillock","Club"),rd=c("Fib","SM","Endo"),gn=c("B-cells","T-cells","Macrophages","Mast cells"),file=paste0(i,".",substr(j,4,6),substr(j,9,9)))
+#     }
+#   }
+#   
+#   write.table(table(sc10x@meta.data[,"samples"],sc10x@meta.data[,"Merge"]),file=paste0("./analysis/table/Table_samples_Merge",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+#   write.table(round(prop.table(table(sc10x@meta.data[,"samples"],sc10x@meta.data[,"Merge"]),1)*100,1),file=paste0("./analysis/table/ProbTable_samples_Merge",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+   
   assign(paste0("sc10x.",i,".analized"),sc10x)
   assign(paste0("sc10x.Epi.",i,".analized"),sc10x.Epi)
+  assign(paste0("sc10x.nEpi.",i,".analized"),sc10x.nEpi)
   assign(paste0("sc10x.St.",i,".analized"),sc10x.St)
   assign(paste0("sc10x.Leu.",i,".analized"),sc10x.Leu)
   assign(paste0("results.cor.Lin.",i),results.cor.Lin)
@@ -341,6 +455,13 @@ for (i in c("Pb","Pc","Pd")){
   assign(paste0("results.clust.Epi.id.",i),results.clust.Epi.id)
   assign(paste0("results.cor.St.",i),results.cor.St)
   assign(paste0("results.clust.St.id.",i),results.clust.St.id)
+  assign(paste0("results.cor.Leu.",i),results.cor.Leu)
+  assign(paste0("results.clust.Leu.id.",i),results.clust.Leu.id)
+  assign(paste0("results.cor.Leu.s.",i),results.cor.Leu.s)
+  assign(paste0("results.clust.Leu.s.id.",i),results.clust.Leu.s.id)
+  assign(paste0("results.cor.Leu.l.",i),results.cor.Leu.l)
+  assign(paste0("results.clust.Leu.l.id.",i),results.clust.Leu.l.id)
+
   rm(sc10x.sub)  
   rm(sc10x)
   rm(sc10x.Epi)
@@ -349,13 +470,21 @@ for (i in c("Pb","Pc","Pd")){
   rm(results.cor.Lin)
   rm(results.cor.Epi)
   rm(results.cor.St)
+  rm(results.cor.Leu)
+  rm(results.cor.Leu.s)
+  rm(results.cor.Leu.l)
   rm(results.clust.Lin.id)
   rm(results.clust.Epi.id)
   rm(results.clust.St.id)
+  rm(results.clust.Leu.id)
+  rm(results.clust.Leu.s.id)
+  rm(results.clust.Leu.l.id)
   rm(min.all)
   rm(min.epi)
+  rm(min.nepi)
   rm(min.st)
-  rm(i)
+  rm(min.leu)
 }
+rm(i)
 save.image(file="./analysis/sc10x.analized.RData")