From fc99994121d2104cad8cb77fbc6b766494e805dd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 8 Jul 2018 22:15:26 -0500
Subject: [PATCH] Add secondary analysis to DPr bash script
---
bash.scripts/sc_TissueMapper-DPrF.sh | 4 +++-
r.scripts/sc-TissueMapper.R | 5 ++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/bash.scripts/sc_TissueMapper-DPrF.sh b/bash.scripts/sc_TissueMapper-DPrF.sh
index c38f8a9..ae34cb3 100644
--- a/bash.scripts/sc_TissueMapper-DPrF.sh
+++ b/bash.scripts/sc_TissueMapper-DPrF.sh
@@ -10,4 +10,6 @@
module load R/3.4.1-gccmkl
-Rscript ../r.scripts/sc-TissueMapper_RUN.D.R
\ No newline at end of file
+Rscript ../r.scripts/sc-TissueMapper_RUN.D.R
+Rscript ../r.scripts/sc-TissueMapper_RUN.D.diy.R
+Rscript ../r.scripts/sc-TissueMapper_RUN.D.pseudotime.R
\ No newline at end of file
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index 1ee7a08..cf280c0 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/r.scripts/sc-TissueMapper.R
@@ -1133,6 +1133,5 @@ scPseudotime <- function(sc10x,i,ds){
BEAM_res <- BEAM(scMonocle,branch_point=1,cores=50)
BEAM_res <- BEAM_res[order(BEAM_res$qval),]
BEAM_res <- BEAM_res[,c("gene_short_name","pval","qval")]
- plot_genes_branched_heatmap(scMonocle[rownames(subset(BEAM_res,qval<1e-4)),],branch_point=1,num_clusters=5,cores=50,use_gene_short_name=TRUE,show_rownames=TRUE)
-
-}
\ No newline at end of file
+ #plot_genes_branched_heatmap(scMonocle[rownames(subset(BEAM_res,qval<1e-4)),],branch_point=1,num_clusters=5,cores=50,use_gene_short_name=TRUE,show_rownames=TRUE)
+}
--
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