Reset parameters for D17 to work

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -92,7 +92,7 @@ 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=0.8,type='numeric',help="Max variance cutoff for PCs to use, 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"),
@@ -180,8 +180,8 @@ if (any(levels(sc10x@ident)=="Unknown")){
 #pc.use.epi <- results[[3]]
 #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=0.5,folder="epi")
+#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=0.5,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)
@@ -231,8 +231,8 @@ rm(OE.cells)
 #pc.use.st <- results[[3]]
 #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=0.5,folder="st")
+#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=0.5,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)