Remove low end cutoff for cell with low gene content

r.scripts/sc-TissueMapper_RUN.DS_D17.R

@@ -94,7 +94,7 @@ if (!dir.exists("./analysis/pseudotime")){
 option_list=list(
   make_option("--p",action="store",default="DPrF",type='character',help="Project Name"),
   make_option("--g",action="store",default="ALL",type='character',help="Group To analyze"),
-  make_option("--lg",action="store",default=500,type='integer',help="Threshold for cells with minimum genes"),
+  make_option("--lg",action="store",default=0,type='integer',help="Threshold for cells with minimum genes"),
   make_option("--hg",action="store",default=3000,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"),
@@ -114,6 +114,7 @@ option_list=list(
 )
 opt=parse_args(OptionParser(option_list=option_list))
 rm(option_list)
+if (opt$lg==0){opt$lg=-Inf}
 if (opt$lm==0){opt$lm=-Inf}
 
 sc10x.data <- Read10X(data.dir="./analysis/DATA/10x/filtered_gene_bc_matrices/GRCh38/")