Stop recalculation of hvg and PCA in subcluster, use PCs previously calcualted from combined data

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -92,13 +92,13 @@ option_list=list(
   make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
   make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
   make_option("--stg",action="store",default="go",type='character',help="Geneset to use for stress ID"),
-  make_option("--hpc.poststress",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
-  make_option("--res.poststress",action="store",default=0.1,type='numeric',help="Resolution to cluster, post-stress"),
+  make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
+  make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
   make_option("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
   make_option("--hpc.epi",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
-  make_option("--res.epi",action="store",default=0.1,type='numeric',help="Resolution to cluster, Epi"),
+  make_option("--res.epi",action="store",default=0.2,type='numeric',help="Resolution to cluster, Epi"),
   make_option("--hpc.st",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, St"),
-  make_option("--res.st",action="store",default=0.1,type='numeric',help="Resolution to cluster, St")
+  make_option("--res.st",action="store",default=0.2,type='numeric',help="Resolution to cluster, St")
   )
 opt=parse_args(OptionParser(option_list=option_list))
 rm(option_list)
@@ -174,13 +174,13 @@ if (any(levels(sc10x@ident)=="Unknown")){
   sc10x.St <- scSubset(sc10x,i="Lin",g="St")
 }
 
-results <- scPC(sc10x.Epi,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc.epi,file="Epi")
-sc10x.Epi <- results[[1]]
-genes.hvg.epi <- results[[2]]
-pc.use.epi <- results[[3]]
-rm(results)
+#results <- scPC(sc10x.Epi,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc.epi,file="Epi")
+#sc10x.Epi <- results[[1]]
+#genes.hvg.epi <- results[[2]]
+#pc.use.epi <- results[[3]]
+#rm(results)
 
-sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=opt$res.epi,folder="epi")
+sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
 
 gene.set1 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
@@ -223,13 +223,13 @@ rm(plot)
 rm(OE)
 rm(OE.cells)
 
-results <- scPC(sc10x.St,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc.st,file="St")
-sc10x.St <- results[[1]]
-genes.hvg.st <- results[[2]]
-pc.use.st <- results[[3]]
-rm(results)
+#results <- scPC(sc10x.St,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc.st,file="St")
+#sc10x.St <- results[[1]]
+#genes.hvg.st <- results[[2]]
+#pc.use.st <- results[[3]]
+#rm(results)
 
-sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.st,res.use=opt$res.st,folder="st")
+sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=opt$res.st,folder="st")
 
 gene.set1 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set1 <- as.list(gene.set1[-1,])