Update DPr analysis

r.scripts/sc-TissueMapper_RUN.D.R

@@ -147,6 +147,11 @@ sc10x <- results[[1]]
 genes.hvg.cca <- results[[2]]
 rm(results)
 
+rm(sc10x.D17)
+rm(sc10x.D27)
+
+save(sc10x,file="./analysis/sc10x.aggr.Rda")
+
 results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="pre.stress",cca=TRUE)
 sc10x <- results[[1]]
 genes.hvg <- results[[2]]
@@ -171,6 +176,8 @@ if (opt$st==TRUE){
   sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=opt$res.poststress,folder="post.stress")
 }
 
+save(sc10x,file="./analysis/sc10x.stress.Rda")
+
 gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set1 <- gene.set1[1]
 gene.set1 <- as.list(gene.set1)
@@ -203,6 +210,7 @@ if (any(levels(sc10x@ident)=="Unknown")){
 #rm(results)
 
 sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
+#sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.2,folder="epi")
 sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
 sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
 
@@ -241,6 +249,7 @@ rm(gene.set)
 #rm(results)
 
 sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.1,folder="st")
+#sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.2,folder="st")
 sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.5,folder="st")
 sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="st")