--- a/wrapper.sh	Fri May 22 09:06:04 2015 -0400
+++ b/wrapper.sh	Tue May 26 10:37:51 2015 -0400
@@ -52,7 +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>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -86,7 +86,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -96,7 +96,7 @@
 	echo "<a href='${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"
+	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	
 	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
 	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
@@ -104,7 +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>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -138,7 +138,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -148,7 +148,7 @@
 	echo "<a href='${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 "${scatterplot_tab}</tr></table></div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</html>" >> "$html"