Mercurial > repos > davidvanzessen > plotting_merged
diff r_wrapper.sh @ 31:d26e8c208b5f draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 08 Nov 2013 05:29:20 -0500 |
| parents | fb03be3fa862 |
| children | 46c5d9d396a5 |
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--- a/r_wrapper.sh Fri Nov 08 05:29:02 2013 -0500 +++ b/r_wrapper.sh Fri Nov 08 05:29:20 2013 -0500 @@ -1,5 +1,35 @@ #!/bin/bash +echo $1 +echo $2 +echo $3 + +inputFile=$1 +outputFile=$2 +outputDir=$3 dir="$(cd "$(dirname "$0")" && pwd)" -Rscript --verbose $dir/RScript.r $1 "$2.png" 2>&1 -mv -f "$2.png" $2 +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_$sample.png" "$outputDir/VD_$sample.png" + echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" + echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" + echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile + count=$((count+1)) +done +echo "</table>" >> $outputFile + +echo "</html>" >> $2 +