From caf53b7104ccd76ea2751ec9a083fa9d6d408a1a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 17 Oct 2018 23:43:26 -0500
Subject: [PATCH] Change post stress res to 1 and fix Pd subset
---
r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R b/r.scripts/sc-TissueMapper_RUN.PdPbPc.Pd.R
index 79124bc..dddb26a 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)
--
GitLab