--- a/wrapper.sh	Mon Aug 22 07:00:23 2016 -0400
+++ b/wrapper.sh	Mon Aug 22 09:11:17 2016 -0400
@@ -237,6 +237,11 @@
 	
 	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
 	
+	echo "---------------- pattern_plots.r ----------------"
+	echo "---------------- pattern_plots.r ----------------<br />" >> $log
+
+	Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
+	
 	echo "<table class='pure-table pure-table-striped'>" >> $output
 	echo "<thead><tr><th>info</th>" >> $output
 	for gene in ${genes[@]}
@@ -262,6 +267,10 @@
 	#echo "<a href='data_${func}.txt'>Download data</a>" >> $output
 done
 
+echo "<img src='plot1.png' /><br />" >> $output
+echo "<img src='plot2.png' /><br />" >> $output
+echo "<img src='plot3.png' /><br />" >> $output
+
 echo "</div>" >> $output #SHM overview tab end
 
 echo "---------------- images ----------------"
@@ -361,6 +370,9 @@
 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output