Change hvg cutoffs

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -83,9 +83,9 @@ 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=0.1,type='numeric',help="x low threshold for hvg selection"),
+  make_option("--hx",action="store",default=4,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=50,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"),
@@ -351,4 +351,4 @@ save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
 rm(list=ls(pattern="^genes.deg"))
 save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
 rm(list=ls(pattern="^sc10x"))
-save.image(file="./analysis/Data.RData")
\ No newline at end of file
+save.image(file="./analysis/Data.RData")

r.scripts/sc-TissueMapper_RUN.D27.R

@@ -83,9 +83,9 @@ 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=0.1,type='numeric',help="x low threshold for hvg selection"),
+  make_option("--hx",action="store",default=4,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=50,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"),
@@ -96,9 +96,9 @@ option_list=list(
   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=0.7,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("--res.epi",action="store",default=0.2,type='numeric',help="Resolution to cluster, Epi"),
   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")
+  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)