Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
changeset 31:ce8bd23d0335 draft
Uploaded
author | davidvanzessen |
---|---|
date | Tue, 02 Jun 2015 05:26:52 -0400 |
parents | 45554fd15511 |
children | dde5ec847549 |
files | RScript.r wrapper.sh |
diffstat | 2 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- 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))
--- 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"