Previous commit was for DPrF.2, this one is the same to DPrF3

r.scripts/sc-TissueMapper_RUN.D3.R

@@ -100,12 +100,12 @@ option_list=list(
   make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
   make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
   #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=0.1,type='numeric',help="Resolution to cluster, post-stress"),
-  make_option("--ds",action="store",default=50000,type='integer',help="Number of cells to downsample"),
+  make_option("--res.poststress",action="store",default=0.2,type='numeric',help="Resolution to cluster, post-stress"),
+  make_option("--ds",action="store",default=25000,type='integer',help="Number of cells to downsample"),
   #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=0.1,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=0.85,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)