From 410c66956ca6f8cd8a2dee3c44cf87d4305153fa Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Wed, 26 Nov 2014 09:54:02 +0100
Subject: [PATCH] cont. rna-seq workflow
---
R/utils/spinr.R | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/R/utils/spinr.R b/R/utils/spinr.R
index 0366166..44e857c 100644
--- a/R/utils/spinr.R
+++ b/R/utils/spinr.R
@@ -11,10 +11,10 @@ options(width=150)
## better table css: http://www.stat.ubc.ca/~jenny/STAT545A/topic10_tablesCSS.html
spin(rScript, knit=F)
-mdScript <- str_replace(rScript, "[.]R$", ".Rmd")
+rmdScript <- str_replace(rScript, "[.]R$", ".Rmd")
-system(paste("mv", mdScript, "tmp.Rmd"))
-system(paste("cat tmp.Rmd | grep -Ev '^#+$' | grep -Fv '#!/usr/bin/env Rscript' >", basename(mdScript)))
+system(paste("mv", rmdScript, "tmp.Rmd"))
+system(paste("cat tmp.Rmd | grep -Ev '^#+$' | grep -Fv '#!/usr/bin/env Rscript' >", basename(rmdScript)))
file.remove("tmp.Rmd")
cssHeader='
@@ -27,6 +27,8 @@ cssHeader='
## custom title http://stackoverflow.com/questions/14124022/setting-html-meta-elements-with-knitr
opts_chunk$set(cache = TRUE, fig.width=10, width=120)
-knit2html(basename(mdScript), header=cssHeader)
+knit2html(basename(rmdScript), header=cssHeader)
-file.remove(basename(mdScript))
+file.remove(basename(rmdScript))
+file.remove(basename(str_replace(rScript, "[.]R$", ".md")
+))
--
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