From e86b31636932ff652f0cbc4f26e7a076e379db9b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 15 Aug 2018 22:20:55 -0500
Subject: [PATCH] Fix opt default for D2 --st
---
r.scripts/sc-TissueMapper_RUN.D2.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.D2.R b/r.scripts/sc-TissueMapper_RUN.D2.R
index 60600a5..e42dc5a 100644
--- a/r.scripts/sc-TissueMapper_RUN.D2.R
+++ b/r.scripts/sc-TissueMapper_RUN.D2.R
@@ -97,7 +97,7 @@ option_list=list(
make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
make_option("--hpc",action="store",default=0.85,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("--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("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.2,type='numeric',help="Resolution to cluster, post-stress"),
--
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