Change res for St to 0.3 and change cutoff for NE to 0.1% in D17

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -102,7 +102,7 @@ option_list=list(
   #make_option("--hpc.epi",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
   make_option("--res.epi",action="store",default=0.2,type='numeric',help="Resolution to cluster, Epi"),
   #make_option("--hpc.st",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, St"),
-  make_option("--res.st",action="store",default=0.2,type='numeric',help="Resolution to cluster, St")
+  make_option("--res.st",action="store",default=0.3,type='numeric',help="Resolution to cluster, St")
   )
 opt=parse_args(OptionParser(option_list=option_list))
 rm(option_list)
@@ -250,7 +250,7 @@ results.clust.St.go.id <- results[[3]]
 rm(results)
 rm(gene.set)
 
-sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=0.95)
+sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=0.999)
 
 sc10x.Epi <- scMergeSubClust(sc10x.Epi,i="Epi.dws.sub",g=c("BE","LE"),nm="Merge")