--- a/wrapper.sh	Tue May 19 08:13:49 2015 -0400
+++ b/wrapper.sh	Fri May 22 09:06:04 2015 -0400
@@ -5,12 +5,13 @@
 outputDir=$3
 min_freq=$4
 min_cells=$5
+merge_on="$6"
 
 dir="$(cd "$(dirname "$0")" && pwd)"
 mkdir $outputDir
 
 
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells "${merge_on}" 2>&1
 cp $dir/jquery-1.11.0.min.js $outputDir
 cp $dir/script.js $outputDir
 cp $dir/style.css $outputDir
@@ -51,6 +52,7 @@
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
 	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -82,7 +84,10 @@
 		echo "<td>$sum</td>" >> "$html"
 		echo "<td>${percent}&#37;</td>" >> "$html"
 		echo "</tr>" >> "$html"
-		oldLocus="$locus"	
+		oldLocus="$locus"
+		if [ "${cut_off_value}" == "0" ] ; then
+			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /><br />"
+		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
@@ -91,6 +96,7 @@
 	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
+	echo "${scatterplot_tab}</div>" >> "$html"
 	
 	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
 	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
@@ -98,6 +104,7 @@
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
 	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -130,6 +137,9 @@
 		echo "<td>${percent}&#37;</td>" >> "$html"
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
+		if [ "${cut_off_value}" == "0" ] ; then
+			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /><br />"
+		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
@@ -138,6 +148,7 @@
 	echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
+	echo "${scatterplot_tab}</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</html>" >> "$html"
@@ -146,7 +157,7 @@
 html="index.html"
 echo "<html>" > $html
 echo "<table>" >> "$html"
-echo "<tr><td><b>Singles:</b></td></tr>" >> "$html"
+echo "<tr><td><b>Singles (<a href='singles_freq_scatterplot.png'>Frequency scatterplot</a>, <a href='singles_reads_scatterplot.png'>Reads scatterplot</a>):</b></td></tr>" >> "$html"
 for patient in "${singles[@]}"
 do
 	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"