From 4eca3bdebd63fd634c592c1d4ee45ed147c74271 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Fri, 29 Jan 2016 13:55:20 +0100
Subject: [PATCH] plot mroe terms
---
common/plot_kegg_pathways.R | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/common/plot_kegg_pathways.R b/common/plot_kegg_pathways.R
index 5a14366..cb28b23 100755
--- a/common/plot_kegg_pathways.R
+++ b/common/plot_kegg_pathways.R
@@ -13,18 +13,18 @@ Usage: plot_kegg_pathways.R <overlay_data_tsv> <pathways>...
opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/bio/diffex_commons.R")
+if(!require(devtools)) install.packages("devtools")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/bio/diffex_commons.R")
require_auto(knitr)
require_auto(DT)
-require_auto(readr)
## todo why is tidyr not processing an empty dataframe
-keggPathways <- opts$pathways
+keggPathways <- opts$pathways %>% str_split(",") %>% unlist()
##+ results='asis'
#if(!exists("keggPathways") | nrow(keggPathways)==0){
--
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