Mercurial > repos > davidvanzessen > test_plotting_merged
diff r_wrapper.sh @ 0:0e6f33e21c60 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 09 Oct 2013 04:31:48 -0400 |
| parents | |
| children | 10cfa5e9186e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_wrapper.sh Wed Oct 09 04:31:48 2013 -0400 @@ -0,0 +1,35 @@ +#!/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 "<html>" >> $2 +echo "<img src='VPlot.png'/>" >> $2 +echo "<img src='DPlot.png'/>" >> $2 +echo "<img src='JPlot.png'/>" >> $2 + +samples=`cat $outputDir/samples.txt` +count=1 +echo "<table border='1'>" >> $outputFile +for sample in $samples; do + echo "<tr><td colspan='3' height='100'></td>" >> $outputFile + echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile + 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>" >> $outputFile + mv "$outputDir/HeatmapVD$count.png" "$outputDir/VD_$sample.png" + echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapVJ$count.png" "$outputDir/VJ_$sample.png" + echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapDJ$count.png" "$outputDir/DJ_$sample.png" + echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile + count=$((count+1)) +done +echo "</table>" >> $outputFile + +echo "</html>" >> $2 +