# HG changeset patch
# User davidvanzessen
# Date 1386680134 18000
# Node ID a43100e5d0327ae577bd7a61a7292386b43fca21
# Parent 0544b052af07924c78f1d45fd99f193530510074
Deleted selected files
diff -r 0544b052af07 -r a43100e5d032 plotting_merged.xml
--- a/plotting_merged.xml Tue Dec 10 07:26:10 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-
- Creating a graph of the merged reports.
-
- r_wrapper.sh $in_file $out_file $out_file.files_path
-
-
-
-
-
-
-
-
- Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
-
-
diff -r 0544b052af07 -r a43100e5d032 r_wrapper.sh
--- a/r_wrapper.sh Tue Dec 10 07:26:10 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/bin/bash
-echo $1
-echo $2
-echo $3
-
-inputFile=$1
-outputFile=$2
-outputDir=$3
-dir="$(cd "$(dirname "$0")" && pwd)"
-mkdir $3
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1
-echo "" >> $2
-echo "
" >> $2
-echo "
" >> $2
-echo "
" >> $2
-
-samples=`cat $outputDir/samples.txt`
-count=1
-echo "" >> $outputFile
-for sample in $samples; do
- echo " | " >> $outputFile
- echo "
$sample |
" >> $outputFile
- echo "V-D Heatmap: | V-J Heatmap: | D-J Heatmap: |
" >> $outputFile
- mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
- echo " | " >> $outputFile
- mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
- echo " | " >> $outputFile
- mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
- echo " |
" >> $outputFile
- count=$((count+1))
-done
-echo "
" >> $outputFile
-
-echo "" >> $2
-