Tweak D17 analysis

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -84,20 +84,20 @@ option_list=list(
   make_option("--lm",action="store",default=0,type='numeric',help="Threshold for cells with minimum %mito genes"),
   make_option("--hm",action="store",default=0.1,type='numeric',help="Threshold for cells with maximum %mito genes"),
   make_option("--lx",action="store",default=0.0125,type='numeric',help="x low threshold for hvg selection"),
-  make_option("--hx",action="store",default=3,type='numeric',help="x high threshold for hvg selection"),
+  make_option("--hx",action="store",default=3.5,type='numeric',help="x high threshold for hvg selection"),
   make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
   make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
   make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
-  make_option("--hpc",action="store",default=0.7,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
+  make_option("--hpc",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
   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=0.7,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("--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("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
-  make_option("--hpc.epi",action="store",default=0.7,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
+  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("--hpc.st",action="store",default=0.7,type='numeric',help="Max variance cutoff for PCs to use, St"),
+  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")
   )
 opt=parse_args(OptionParser(option_list=option_list))
@@ -129,14 +129,14 @@ rm(results)
 
 results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="pre.stress")
 sc10x <- results[[1]]
-genes.hvg <- results[[2]]
-pc.use <- results[[3]]
+genes.hvg.prestress <- results[[2]]
+pc.use.prestress <- results[[3]]
 rm(results)
 
-sc10x <- scCluster(sc10x,pc.use=pc.use,res.use=opt$res.prestress,folder="pre.stress")
+sc10x <- scCluster(sc10x,pc.use=pc.use.prestress,res.use=opt$res.prestress,folder="pre.stress")
 
 if (opt$st==TRUE){
-  results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,pc.use=pc.use)
+  results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,pc.use=pc.use.prestress)
   sc10x <- results[[1]]
   counts.cell.filtered.stress <- results[[2]]
   sc10x.Stress <- results[[3]]