Fix opt default for D2 --st

r.scripts/sc-TissueMapper_RUN.D2.R

@@ -97,7 +97,7 @@ option_list=list(
   make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
   make_option("--hpc",action="store",default=0.85,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("--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=0.2,type='numeric',help="Resolution to cluster, post-stress"),