--- a/wrapper.sh	Tue Jun 21 05:30:16 2016 -0400
+++ b/wrapper.sh	Wed Jun 22 10:07:28 2016 -0400
@@ -148,7 +148,10 @@
 echo "---------------- aa_histogram.r ----------------"
 echo "---------------- aa_histogram.r ----------------<br />" >> $output
 
-Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
+Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png "" 2>&1
+Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1
+Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1
+Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1
 
 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
 
@@ -279,6 +282,12 @@
 then
 	echo "<img src='aa_histogram.png'/><br />" >> $output
 	echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
+	echo "<img src='aa_histogram_ca.png'/><br />" >> $output
+	echo "<a href='aa_histogram_ca.txt'>download data</a><br />" >> $output
+	echo "<img src='aa_histogram_cg.png'/><br />" >> $output
+	echo "<a href='aa_histogram_cg.txt'>download data</a><br />" >> $output
+	echo "<img src='aa_histogram_cm.png'/><br />" >> $output
+	echo "<a href='aa_histogram_cm.txt'>download data</a><br />" >> $output
 fi
 
 for gene in ${genes[@]}