diff report_clonality/r_wrapper.sh @ 8:8cbc1a8d27ae draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Fri Dec 16 09:01:40 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Mon Dec 19 08:50:31 2016 -0500
@@ -106,7 +106,7 @@
 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
 
-echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
+
 echo "<img src='VFPlot.png'/>" >> $outputFile
 if [[ "$useD" == "true" ]] ; then
 	echo "<img src='DFPlot.png'/>" >> $outputFile
@@ -116,8 +116,21 @@
 	echo "<img src='DPlot.png'/>" >> $outputFile
 fi
 echo "<img src='JPlot.png'/>" >> $outputFile
+echo "</div>" >> $outputFile
+
+echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
+echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
 echo "<img src='AAComposition.png'/>" >> $outputFile
 echo "<img src='DReadingFrame.png'/>" >> $outputFile
+
+echo "<table class='pure-table pure-table-striped'>" >> $outputFile
+echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
+while IFS=, read Sample median
+do
+	echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
+done < $outputDir/AAMedianBySample.csv
+echo "</table>" >> $outputFile
+
 echo "</div>" >> $outputFile
 
 #Heatmaps