Mercurial > repos > davidvanzessen > test_plotting_merged

comparison r_wrapper.sh @ 0:0e6f33e21c60 draft

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author davidvanzessen
date Wed, 09 Oct 2013 04:31:48 -0400
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children 10cfa5e9186e
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-1:000000000000 0:0e6f33e21c60
1 #!/bin/bash
2 echo $1
3 echo $2
4 echo $3
5
6 inputFile=$1
7 outputFile=$2
8 outputDir=$3
9 dir="$(cd "$(dirname "$0")" && pwd)"
10 mkdir $3
11 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1
12 echo "<html>" >> $2
13 echo "<img src='VPlot.png'/>" >> $2
14 echo "<img src='DPlot.png'/>" >> $2
15 echo "<img src='JPlot.png'/>" >> $2
16
17 samples=`cat $outputDir/samples.txt`
18 count=1
19 echo "<table border='1'>" >> $outputFile
20 for sample in $samples; do
21 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
22 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
23 echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
24 mv "$outputDir/HeatmapVD$count.png" "$outputDir/VD_$sample.png"
25 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
26 mv "$outputDir/HeatmapVJ$count.png" "$outputDir/VJ_$sample.png"
27 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
28 mv "$outputDir/HeatmapDJ$count.png" "$outputDir/DJ_$sample.png"
29 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
30 count=$((count+1))
31 done
32 echo "</table>" >> $outputFile
33
34 echo "</html>" >> $2
35