Updata PdPbPc code... res etc

r.scripts/sc-TissueMapper_RUN.PdPbPc.Pb.R

@@ -114,9 +114,9 @@ opt=parse_args(OptionParser(option_list=option_list))
 rm(option_list)
 if (opt$lm==0){opt$lm=-Inf}
 
-sc10x <- scLoad("Pb",sub="Pb)
+sc10x <- scLoad("Pb",sub="Pb")
 
-sc10x <- scSubset(sc10x,i="Glandular",g="Glandular")
+#sc10x <- scSubset(sc10x,i="Glandular",g="Glandular")
 
 if (opt$cc==TRUE){
   results <- scCellCycle(sc10x)
@@ -145,9 +145,9 @@ if (opt$cc==TRUE){
 }
 gc()
 
-sc10x.B327 <- scSubset(sc10x,"samples","BPH327PrGF_Via")
-sc10x.B340 <- scSubset(sc10x,"samples","BPH340PrSF_Via")
-sc10x.B342 <- scSubset(sc10x,"samples","BPH342PrF_Via")
+sc10x.B327 <- scSubset(sc10x,"B327","B327")
+sc10x.B340 <- scSubset(sc10x,"B340","B340")
+sc10x.B342 <- scSubset(sc10x,"B342","B342")
 
 results <- sc3CCA(sc10x.B327,sc10x.B340,sc10x.B342,"B327","B340","B342",cc=opt$cc,cca=opt$cca,acca=opt$acca,lx=opt$lx,hx=opt$hx,ly=opt$ly)
 sc10x <- results[[1]]

r.scripts/sc-TissueMapper_RUN.PdPbPc.Pc.R

@@ -171,4 +171,4 @@ if (opt$st==TRUE){
 }
 
 sc10x.Pc <- sc10x
-save(sc10x,file="./analysis/sc10x.Pc.Rda")
+save(sc10x.Pc,file="./analysis/sc10x.Pc.Rda")

r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R

@@ -169,4 +169,4 @@ if (opt$st==TRUE){
 }
 
 sc10x.Pd <- sc10x
-save(sc10x,file="./analysis/sc10x.Pd.Rda")
+save(sc10x.Pd,file="./analysis/sc10x.Pd.Rda")

r.scripts/sc-TissueMapper_RUN.PdPbPc.R

@@ -111,7 +111,7 @@ option_list=list(
   make_option("--st",action="store",default=TRUE,type='logical',help="Remove stressed cells?"),
   make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
   make_option("--cut.stress",action="store",default=0.9,type='numeric',help="Cutoff for stress score"),
-  make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
+  make_option("--res.poststress",action="store",default=0.75,type='numeric',help="Resolution to cluster, post-stress"),
   make_option("--cut.ne",action="store",default=0.999,type='numeric',help="Cutoff for NE score")
 )
 opt=parse_args(OptionParser(option_list=option_list))
@@ -141,7 +141,7 @@ for (i in c("Pb","Pc","Pd")){
 
   sc10x <- get(paste0("sc10x.",i))
     
-  sc10x <- scCluster(sc10x,pc.use=opt$acca,res.use=0.5,folder=paste0("post.stress/",i),red="cca.aligned")
+  sc10x <- scCluster(sc10x,pc.use=opt$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)
   gene.set1 <- as.list(gene.set1)
@@ -154,7 +154,7 @@ for (i in c("Pb","Pc","Pd")){
   rm(gene.set1)
   gc()
   min.all <- min(table(sc10x@meta.data[,paste0("res",0.5)]))
-  results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder=paste0("lin/",i))
+  results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Lin",folder=paste0("lin/",i))
   sc10x <- results[[1]]
   results.cor.Lin <- results[[2]]
   results.clust.Lin.id <- results[[3]]
@@ -213,7 +213,7 @@ 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=min.epi,nm="Epi.dws.sc",folder=paste0("epi/",i))
+  results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Epi.dws.sc",folder=paste0("epi/",i))
   sc10x.Epi <- results[[1]]
   results.cor.Epi <- results[[2]]
   results.clust.Epi.id <- results[[3]]
@@ -271,7 +271,7 @@ for (i in c("Pb","Pc","Pd")){
   rm(gene.set1)
   gc()
   min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
-  results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=min.st,nm="St.dws.sc",folder=paste0("st/",i))
+  results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="St.dws.sc",folder=paste0("st/",i))
   sc10x.St <- results[[1]]
   results.cor.St <- results[[2]]
   results.clust.St.id <- results[[3]]
@@ -309,6 +309,23 @@ for (i in c("Pb","Pc","Pd")){
       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=",")