--- a/wrapper.sh	Tue Mar 28 08:25:36 2017 -0400
+++ b/wrapper.sh	Tue Apr 11 08:02:17 2017 -0400
@@ -176,6 +176,13 @@
 echo "R mutation analysis"
 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
 
+echo "---------------- plot_pdfs.r ----------------"
+echo "---------------- plot_pdfs.r ----------------<br />" >> $log
+
+echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
+
+Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
+
 echo "---------------- shm_csr.py ----------------"
 echo "---------------- shm_csr.py ----------------<br />" >> $log
 
@@ -249,7 +256,7 @@
 	echo "---------------- pattern_plots.r ----------------"
 	echo "---------------- pattern_plots.r ----------------<br />" >> $log
 
-	Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/abolute_mutations $outdir/shm_overview.txt 2>&1
+	Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
 	
 	echo "<table class='pure-table pure-table-striped'>" >> $output
 	echo "<thead><tr><th>info</th>" >> $output
@@ -300,7 +307,7 @@
 
 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
-echo "<a href='abolute_mutations.pdf'><img src='abolute_mutations.png' /></a><br />" >> $output
+echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
 echo "<br />" >> $output
 cat $dir/shm_overview.htm >> $output
 echo "</div>" >> $output #SHM overview tab end
@@ -657,7 +664,7 @@
 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
-echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='abolute_mutations.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
 
 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
 echo "<tr><td>The data  generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output