Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
changeset 8:fa240d1c57a9 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 18 Sep 2014 10:28:24 -0400 |
| parents | 68c6c7624ffc |
| children | 58a28427930e |
| files | RScript.r wrapper.sh |
| diffstat | 2 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/RScript.r Thu Sep 18 08:56:44 2014 -0400 +++ b/RScript.r Thu Sep 18 10:28:24 2014 -0400 @@ -317,17 +317,17 @@ one = dat[dat$Patient == "VanDongen_cALL_14696.1",] two = dat[dat$Patient == "VanDongen_cALL_14696.2",] three = dat[dat$Patient == "VanDongen_cALL_14696.3",] -tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count") +tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count", T) one = dat[dat$Sample == "16278_Left",] two = dat[dat$Sample == "26402_Left",] three = dat[dat$Sample == "26759_Left",] -tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count") +tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count", T) one = dat[dat$Sample == "16278_Right",] two = dat[dat$Sample == "26402_Right",] three = dat[dat$Sample == "26759_Right",] -tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count") +tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count", T) interval = intervalFreq @@ -337,17 +337,17 @@ one = dat[dat$Patient == "VanDongen_cALL_14696.1",] two = dat[dat$Patient == "VanDongen_cALL_14696.2",] three = dat[dat$Patient == "VanDongen_cALL_14696.3",] -tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", T) +tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", F) one = dat[dat$Sample == "16278_Left",] two = dat[dat$Sample == "26402_Left",] three = dat[dat$Sample == "26759_Left",] -tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", T) +tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", F) one = dat[dat$Sample == "16278_Right",] two = dat[dat$Sample == "26402_Right",] three = dat[dat$Sample == "26759_Right",] -tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", T) +tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", F)
--- a/wrapper.sh Thu Sep 18 08:56:44 2014 -0400 +++ b/wrapper.sh Thu Sep 18 10:28:24 2014 -0400 @@ -227,8 +227,8 @@ echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html echo "</div>" >> $html echo "<div class='tabbertab' title='Graphs frequency'>" >> $html - echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html - echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html + echo "<a href='${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 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt echo "<div class='tabbertab' title='Data reads'>" >> $html @@ -277,8 +277,8 @@ echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html echo "</div>" >> $html echo "<div class='tabbertab' title='Graphs reads'>" >> $html - echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html - echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html + echo "<a href='${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 "</div>" >> $html echo "</div>" >> $html echo "</html>" >> $html