# HG changeset patch
# User davidvanzessen
# Date 1433237212 14400
# Node ID ce8bd23d033537c716a5ef66b9a4b47b14c0748a
# Parent  45554fd15511dcaad82141f70489b82bd90a68ad
Uploaded

diff -r 45554fd15511 -r ce8bd23d0335 RScript.r
--- a/RScript.r	Tue May 26 10:37:51 2015 -0400
+++ b/RScript.r	Tue Jun 02 05:26:52 2015 -0400
@@ -288,7 +288,7 @@
 
 cat("</table></html>", file=logfile, append=T)
 
-scales = 10^(0:ceiling(log10(max(single_patients$normalized_read_count))))
+scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
 p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
 p = p + geom_point(aes(colour=type), position="jitter")
 p = p + xlab("In one or both samples") + ylab("Reads")
@@ -447,7 +447,7 @@
       p = NULL
       if(nrow(scatterplot_locus_data) != 0){
         if(on == "normalized_read_count"){
-          scales = 10^(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
+					scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
           p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
         } else {
           p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 
diff -r 45554fd15511 -r ce8bd23d0335 wrapper.sh
--- a/wrapper.sh	Tue May 26 10:37:51 2015 -0400
+++ b/wrapper.sh	Tue Jun 02 05:26:52 2015 -0400
@@ -197,7 +197,7 @@
 	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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -249,7 +249,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -258,7 +258,7 @@
 	echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
 	echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></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"
@@ -266,7 +266,7 @@
 	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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -318,7 +318,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -327,7 +327,7 @@
 	echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
 	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
-	echo "${scatterplot_tab}</div>" >> "$html"
+	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</html>" >> "$html"