Revert hvg cutoffs in function based pipleine to fix cluster problems

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -83,21 +83,21 @@ option_list=list(
   make_option("--hg",action="store",default=2500,type='integer',help="Threshold for cells with maximum genes"),
   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=0.15,type='numeric',help="x low 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=0.75,type='numeric',help="y low threshold for hvg selection"),
+  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("--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("--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=0.75,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
+  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("--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"),
+  make_option("--hpc.epi",action="store",default=0.7,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=0.85,type='numeric',help="Max variance cutoff for PCs to use, St"),
+  make_option("--hpc.st",action="store",default=0.7,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))