diff --git a/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R b/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R index 79124bc9abbd07a70531cf0687c0582ec08f14c4..dddb26a2b8d746421b2923fca915fd6dd3f5f173 100644 --- a/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R +++ b/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R @@ -107,7 +107,7 @@ 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("--cut.stress",action="store",default=0.9,type='numeric',help="Cutoff for stress score"), - make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"), + make_option("--res.poststress",action="store",default=1,type='numeric',help="Resolution to cluster, post-stress"), make_option("--cut.ne",action="store",default=0.999,type='numeric',help="Cutoff for NE score") ) opt=parse_args(OptionParser(option_list=option_list)) @@ -116,7 +116,7 @@ if (opt$lm==0){opt$lm=-Inf} sc10x <- scLoad("Pd") -sc10x <- scSubset(sc10x,i="Tumor",g="Tumor") +sc10x <- scSubset(sc10x,i="ALL",g="ALL") if (opt$cc==TRUE){ results <- scCellCycle(sc10x)