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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-deeptools">Debian Med / python-deeptools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf">efaae4b3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-23T01:33:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.5.1</pre>
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<h4>22 changed files:</h4>
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<li class="file-stats">
<a href="#3bf02d97dbbf2b872758e8f55e9f2e2f319cc9c4">
.planemo.sh
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<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#3ec39721c34812eb70f07264b96298182b24bca7">
deeptools/_version.py
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<li class="file-stats">
<a href="#6535c71146ed29c18429c39896921c2ac0405ecf">
deeptools/bamPEFragmentSize.py
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<li class="file-stats">
<a href="#f5d86efbc2efe8a8f8bf80196dde3a5a19f11fdf">
deeptools/computeGCBias.py
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<li class="file-stats">
<a href="#419cb713bac82fae39f1b6238833e4b93c9a75fc">
deeptools/computeMatrixOperations.py
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<li class="file-stats">
<a href="#7abbfd754c96a0b533b2bcc3a0f5aac1f2d6de25">
deeptools/correlation.py
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<li class="file-stats">
<a href="#c3e127cb6e22a38fcfb34c58f35844f38c551ebc">
deeptools/correlation_heatmap.py
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<li class="file-stats">
<a href="#94e366580f5a271c89a0fea3629c8e79df36aac2">
deeptools/plotCoverage.py
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<li class="file-stats">
<a href="#9ead2bde87de5736c1b85bb9cf9e6fa9814ce6bd">
deeptools/plotEnrichment.py
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<li class="file-stats">
<a href="#3641adfed9392b31f39826c32f7b6817c2dbe618">
deeptools/plotFingerprint.py
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<li class="file-stats">
<a href="#e6f336c84329d2021242809e76ed32e6ed05fecc">
deeptools/plotHeatmap.py
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<li class="file-stats">
<a href="#933931be8d4eb6bef5ca9c328d98370ed0c3370a">
deeptools/plotProfile.py
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<li class="file-stats">
<a href="#47c155641ae77d95414796ebb02b457b4b587fc2">
deeptools/utilities.py
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<li class="file-stats">
<a href="#abc059e39dfccf4038fabfb18bfb7b5121e4e2e4">
galaxy/wrapper/computeMatrixOperations.xml
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<li class="file-stats">
<a href="#d2de9c6869fd65911899bace5f34a175e96efb2a">
galaxy/wrapper/deepTools_macros.xml
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<li class="file-stats">
<a href="#5bb35761036ed12cc2d6fc54c2928bcdfd2e5071">
galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt
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<li class="file-stats">
<a href="#a5d8ab9e3ca6b3aabfc033e525b08b190362aa98">
galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt
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<li class="file-stats">
<a href="#0fe7a0a47ac88c595cb77d4fe718abef6e1d4b88">
galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular
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<li class="file-stats">
<a href="#e775e2873f0a3295f76cd404ea49d1531c224470">
galaxy/wrapper/test-data/plotPCA_result2.tabular
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</ul>
<h4>Changes:</h4>
<li id="3bf02d97dbbf2b872758e8f55e9f2e2f319cc9c4">
<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#3bf02d97dbbf2b872758e8f55e9f2e2f319cc9c4"><strong>.planemo.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,5 +28,5 @@ else</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell">planemo lint <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">wrappers</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">planemo <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--no_dependency_resolution</span> <span class="nt" style="color: #000080;">--galaxy_branch</span> release_<span class="idiff left">18</span>.0<span class="idiff right">5</span> <span class="nt" style="color: #000080;">--install_galaxy</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">wrappers</span><span class="k" style="font-weight: 600;">}</span> 2>&1 | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"^galaxy"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"^requests"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">planemo <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--no_dependency_resolution</span> <span class="nt" style="color: #000080;">--galaxy_branch</span> release_<span class="idiff left">20</span>.0<span class="idiff right">9</span> <span class="nt" style="color: #000080;">--install_galaxy</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">wrappers</span><span class="k" style="font-weight: 600;">}</span> 2>&1 | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"^galaxy"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"^requests"</span></span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PIPESTATUS</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-eq</span> 0</span></pre>
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<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.5.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">* cmp usage is updated to fit the recent mpl updates.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">* The requirements.txt is updated.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* "NA" occurences in plotFingerprint.py have been replaced by numpy.NAN (PR #1002)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* computeMatrixOperations.xml is fixed (brought up in #1003)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">* plotly error is fixed. (issue #1013)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* relase version is updated in planemo.sh</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* fixed galaxy tests</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">* A bug is taken care of in computeMatrixOperations.py / dataRange</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* in plotProfile.py legen location is changed from auto to best (issue #1042)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">3.5.0</span>
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2
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Fixed a small issue in computeGCBias (issue #969)</span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#3ec39721c34812eb70f07264b96298182b24bca7"><strong>deeptools/_version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file is originally generated from Git information by running 'setup.py</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># version'. Distribution tarballs contain a pre-generated copy of this file.</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.5.<span class="idiff left right">0</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.5.<span class="idiff left right">1</span>'</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -341,7 +341,7 @@ def main(args=None):</td>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFileFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'plotly'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">fig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">go</span><span class="p">.</span><span class="n" style="color: #333;">Figure</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'yaxis1'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Frequency'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'xaxis1'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Fragment Length'</span><span class="p">)</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotTitle</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#f5d86efbc2efe8a8f8bf80196dde3a5a19f11fdf"><strong>deeptools/computeGCBias.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -571,7 +571,7 @@ def plotlyGCbias(file_name, frequencies, reads_per_gc, region_size):</td>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">linspace</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">frequencies</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">trace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">go</span><span class="p">.</span><span class="n" style="color: #333;">Scatter</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">frequencies</span><span class="p">[:,</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">xaxis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'x2'</span><span class="p">,</span> <span class="n" style="color: #333;">yaxis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'y2'</span><span class="p">,</span> <span class="n" style="color: #333;">showlegend</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'rgb(107,174,214)'</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">trace</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"></span>
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<li id="419cb713bac82fae39f1b6238833e4b93c9a75fc">
<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#419cb713bac82fae39f1b6238833e4b93c9a75fc"><strong>deeptools/computeMatrixOperations.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ or</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentDefaultsHelpFormatter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">parents</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">infoArgs</span><span class="p">(),</span> <span class="n" style="color: #333;">relabelArgs</span><span class="p">()],</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Change sample and/or group label information"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'An example usage is:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --samples "sample 1" "sample 2"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'An example usage is:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --sample<span class="idiff left right">Label</span>s "sample 1" "sample 2"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># subset</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -795,10 +795,9 @@ def main(args=None):</td>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">hm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">heatmapper</span><span class="p">.</span><span class="n" style="color: #333;">heatmapper</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matrixFile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">read_matrix_file</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matrixFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'info'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python"> <span class="n" style="color: #333;">printInfo</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'dataRange'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left right">el</span>if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'dataRange'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">printDataRange</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'subset'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python"> <span class="n" style="color: #333;">sIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSampleBounds</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">hm</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#7abbfd754c96a0b533b2bcc3a0f5aac1f2d6de25"><strong>deeptools/correlation.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.cluster.hierarchy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sch</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.stats</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,7 +292,7 @@ class Correlation:</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">link_color_func</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="s" style="color: #d14;">'darkred'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">axdendro</span><span class="p">.</span><span class="n" style="color: #333;">set_xticks</span><span class="p">([])</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">axdendro</span><span class="p">.</span><span class="n" style="color: #333;">set_yticks</span><span class="p">([])</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">colormap</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">copy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">copy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">colormap</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this line simply makes a new cmap, based on the original</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># colormap that goes from 0.0 to 0.9</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -421,7 +422,7 @@ class Correlation:</td>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">'colorbar'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"log10(instances per bin)"</span><span class="p">,</span> <span class="n" style="color: #333;">titleside</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"right"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">showscale</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">plot_title</span><span class="p">,</span> <span class="n" style="color: #333;">showlegend</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">annotations</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">offline</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">plot_filename</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -588,7 +589,7 @@ class Correlation:</td>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">annos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">'yanchor'</span><span class="p">:</span> <span class="s" style="color: #d14;">'bottom'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xref'</span><span class="p">:</span> <span class="s" style="color: #d14;">'paper'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xanchor'</span><span class="p">:</span> <span class="s" style="color: #d14;">'center'</span><span class="p">,</span> <span class="s" style="color: #d14;">'yref'</span><span class="p">:</span> <span class="s" style="color: #d14;">'paper'</span><span class="p">,</span> <span class="s" style="color: #d14;">'text'</span><span class="p">:</span> <span class="s" style="color: #d14;">'PCA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'y'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.25</span><span class="p">,</span> <span class="s" style="color: #d14;">'font'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="mi" style="color: #099;">16</span><span class="p">},</span> <span class="s" style="color: #d14;">'showarrow'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">annos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">'yanchor'</span><span class="p">:</span> <span class="s" style="color: #d14;">'bottom'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xref'</span><span class="p">:</span> <span class="s" style="color: #d14;">'paper'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xanchor'</span><span class="p">:</span> <span class="s" style="color: #d14;">'center'</span><span class="p">,</span> <span class="s" style="color: #d14;">'yref'</span><span class="p">:</span> <span class="s" style="color: #d14;">'paper'</span><span class="p">,</span> <span class="s" style="color: #d14;">'text'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Scree plot'</span><span class="p">,</span> <span class="s" style="color: #d14;">'y'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'x'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.75</span><span class="p">,</span> <span class="s" style="color: #d14;">'font'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="mi" style="color: #099;">16</span><span class="p">},</span> <span class="s" style="color: #d14;">'showarrow'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">offline</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">plotFile</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#c3e127cb6e22a38fcfb34c58f35844f38c551ebc"><strong>deeptools/correlation_heatmap.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ import numpy as np</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.cluster.hierarchy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sch</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">matplotlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">rcParams</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib.colors</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pltcolors</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'pdf.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">42</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'svg.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'none'</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +44,7 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">link_color_func</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="s" style="color: #d14;">'darkred'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">axdendro</span><span class="p">.</span><span class="n" style="color: #333;">set_xticks</span><span class="p">([])</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">axdendro</span><span class="p">.</span><span class="n" style="color: #333;">set_yticks</span><span class="p">([])</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">colormap</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">copy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">copy</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">colormap</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this line simply makes a new cmap, based on the original</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># colormap that goes from 0.0 to 0.9</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#94e366580f5a271c89a0fea3629c8e79df36aac2"><strong>deeptools/plotCoverage.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -320,7 +320,7 @@ def main(args=None):</td>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't clip plots</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y_max</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFileFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"plotly"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'yaxis1'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">y_max</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.10</span><span class="p">))])</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'yaxis2'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFile</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#9ead2bde87de5736c1b85bb9cf9e6fa9814ce6bd"><strong>deeptools/plotEnrichment.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -440,7 +440,7 @@ def plotEnrichment(args, featureCounts, totalCounts, features):</td>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">set_ylim</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">100.0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFileFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'plotly'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFile</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># colors</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#3641adfed9392b31f39826c32f7b6817c2dbe618"><strong>deeptools/plotFingerprint.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,10 +202,10 @@ def getCHANCE(args, idx, mat):</td>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get the index of the reference sample</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">JSDsample</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left">"</span>NA<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"</span>NA<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"</span>NA<span class="idiff right">"</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff">N</span></span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff">N</span></span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff right">N</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">refIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">JSDsample</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">refIdx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idx</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left">"</span>NA<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"</span>NA<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"</span>NA<span class="idiff right">"</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff">N</span></span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff">N</span></span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff right">N</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">subMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">[:,</span> <span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">refIdx</span><span class="p">]])</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">subMatrix</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">subMatrix</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -271,10 +271,10 @@ def getJSD(args, idx, mat):</td>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get the index of the reference sample</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">JSDsample</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left">"</span>NA<span class="idiff right">"</span></span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff right">N</span></span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">refIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bamfiles</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">JSDsample</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">refIdx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idx</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left">"</span>NA<span class="idiff right">"</span></span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff right">N</span></span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># These will hold the coverage histograms</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">chip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">MAXLEN</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -338,7 +338,7 @@ def getJSDcommon(chip, input):</td>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">PMFinput</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.01</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">PMFchip</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.01</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: At least one PMF integral is significantly different from 1! The JSD will not be returned"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left">"</span>NA<span class="idiff right">"</span></span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">NA<span class="idiff right">N</span></span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Compute the JSD from the PMFs</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PMFinput</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">PMFchip</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">2.0</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,7 +430,7 @@ def main(args=None):</td>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotFileFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'plotly'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">fig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">go</span><span class="p">.</span><span class="n" style="color: #333;">Figure</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotTitle</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'xaxis1'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rank"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'yaxis1'</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"fraction w.r.t bin with highest coverage"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#e6f336c84329d2021242809e76ed32e6ed05fecc"><strong>deeptools/plotHeatmap.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,17 +9,17 @@ import matplotlib</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">use</span><span class="p">(</span><span class="s" style="color: #d14;">'Agg'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'pdf.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">42</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="p">.</span><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'svg.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'none'</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cm</span> <span class="c1" style="color: #998; font-style: italic;"># noqa: F401</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib.pyplot</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">plt</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">matplotlib.font_manager</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FontProperties</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib.gridspec</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gridspec</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">matplotlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ticker</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">plotly.offline</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">py</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">plotly.graph_objs</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">go</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># own modules</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cm</span> <span class="c1" style="color: #998; font-style: italic;"># noqa: F401</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parserCommon</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">heatmapper</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptools.heatmapper_utilities</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">plot_single</span><span class="p">,</span> <span class="n" style="color: #333;">plotly_single</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -371,7 +371,7 @@ def plotlyMatrix(hm,</td>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">trace</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">zmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zMinUse</span><span class="p">,</span> <span class="n" style="color: #333;">zmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zMaxUse</span><span class="p">,</span> <span class="n" style="color: #333;">colorscale</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">convertCmap</span><span class="p">(</span><span class="n" style="color: #333;">cmap</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">vmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zMinUse</span><span class="p">,</span> <span class="n" style="color: #333;">vmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zMaxUse</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">dataSummary</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">dataHeatmap</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dataSummary</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">dataSummary</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFilename</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -477,7 +477,8 @@ def plotMatrix(hm, outFileName,</td>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'colorMap'</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">color_map</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'colorMap'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">color_map</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">copy_cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">get_cmap</span><span class="p">(</span><span class="n" style="color: #333;">color_map</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">copy_cmp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">set_bad</span><span class="p">(</span><span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'missingDataColor'</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># nans are printed using this color</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'colorList'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'colorList'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -529,7 +530,6 @@ def plotMatrix(hm, outFileName,</td>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> <span class="n" style="color: #333;">color_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmap_plot</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">arange</span><span class="p">(</span><span class="n" style="color: #333;">numgroups</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">numgroups</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">colorMapDict</span><span class="p">[</span><span class="s" style="color: #d14;">'alpha'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">image_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'plotly'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">plotlyMatrix</span><span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">outFileName</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -735,7 +735,7 @@ def plotMatrix(hm, outFileName,</td>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="python"> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python"> <span class="n" style="color: #333;">ax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">add_subplot</span><span class="p">(</span><span class="n" style="color: #333;">grids</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="python"> <span class="n" style="color: #333;">tick_locator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ticker</span><span class="p">.</span><span class="n" style="color: #333;">MaxNLocator</span><span class="p">(</span><span class="n" style="color: #333;">nbins</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="python"> <span class="n" style="color: #333;">cbar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">img</span><span class="p">,</span> <span class="n" style="color: #333;">cax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">orientation</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'horizontal'</span><span class="p">,</span> <span class="n" style="color: #333;">ticks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tick_locator</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="n" style="color: #333;">cbar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">img</span><span class="p">,</span> <span class="n" style="color: #333;">cax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p">,</span> <span class="n" style="color: #333;">orientation</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'horizontal'</span><span class="p">,</span> <span class="n" style="color: #333;">ticks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tick_locator</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cbar</span><span class="p">.</span><span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">get_xticklabels</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">ticks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cbar</span><span class="p">.</span><span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">get_xticks</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ticks</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -759,7 +759,7 @@ def plotMatrix(hm, outFileName,</td>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">grid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">ax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">add_subplot</span><span class="p">(</span><span class="n" style="color: #333;">grids</span><span class="p">[</span><span class="n" style="color: #333;">grid_start</span><span class="p">:,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">img</span><span class="p">,</span> <span class="n" style="color: #333;">cax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">.</span><span class="n" style="color: #333;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">img</span><span class="p">,</span> <span class="n" style="color: #333;">cax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">box_around_heatmaps</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">subplots_adjust</span><span class="p">(</span><span class="n" style="color: #333;">wspace</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.10</span><span class="p">,</span> <span class="n" style="color: #333;">hspace</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.025</span><span class="p">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.85</span><span class="p">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.04</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.96</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -767,7 +767,7 @@ def plotMatrix(hm, outFileName,</td>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># When no box is plotted the space between heatmaps is reduced</span></span>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">subplots_adjust</span><span class="p">(</span><span class="n" style="color: #333;">wspace</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.05</span><span class="p">,</span> <span class="n" style="color: #333;">hspace</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.85</span><span class="p">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.04</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.96</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">outFileName</span><span class="p">,</span> <span class="n" style="color: #333;">bbox_inches</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tight'</span><span class="p">,</span> <span class="n" style="color: #333;">p<span class="idiff left right">d</span>d_inches</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">dpi</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dpi</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">image_format</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">outFileName</span><span class="p">,</span> <span class="n" style="color: #333;">bbox_inches</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tight'</span><span class="p">,</span> <span class="n" style="color: #333;">p<span class="idiff left">a</span>d_inches</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0<span class="idiff right">.1</span></span><span class="p">,</span> <span class="n" style="color: #333;">dpi</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dpi</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">image_format</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,7 +99,7 @@ class Profile(object):</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">plot_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'lines'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">image_format</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">color_list</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">legend_location</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">auto</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">legend_location</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">best</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">plots_per_row</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">8</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">label_rotation</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">dpi</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -454,7 +454,7 @@ class Profile(object):</td>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">trace</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">trace</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">zmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">vmin</span><span class="p">,</span> <span class="n" style="color: #333;">zmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">vmax</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">out_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -668,7 +668,7 @@ class Profile(object):</td>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python"> <span class="n" style="color: #333;">zmaxUse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_max</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_max</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">trace</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">zmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zminUse</span><span class="p">,</span> <span class="n" style="color: #333;">zmax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">zmaxUse</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">out_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -828,15 +828,16 @@ class Profile(object):</td>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">yMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">yMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">numplots</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plots_per_row</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plots_per_row</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># row = rows - i / self.plots_per_row - 1</span></span>
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plots_per_row</span></span>
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="n" style="color: #333;">xanchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'x{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">yanchor</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'y{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">domainHeight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufferHeight</span><span class="p">)</span></span>
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">domainHeight</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">titleY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">domainHeight</span></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">domainWidth</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufferWidth</span><span class="p">)</span></span>
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'yaxis{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'domain'</span><span class="p">:</span> <span class="n" style="color: #333;">domain</span><span class="p">,</span> <span class="s" style="color: #d14;">'title'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_axis_label</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchor'</span><span class="p">:</span> <span class="n" style="color: #333;">xanchor</span><span class="p">,</span> <span class="s" style="color: #d14;">'autorange'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">domainWidth</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufferWidth</span><span class="p">)</span></span>
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">domainWidth</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"> <span class="n" style="color: #333;">titleX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">domainWidth</span></span>
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'xaxis{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'domain'</span><span class="p">:</span> <span class="n" style="color: #333;">domain</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchor'</span><span class="p">:</span> <span class="n" style="color: #333;">yanchor</span><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -900,7 +901,7 @@ class Profile(object):</td>
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">yRange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_max</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">y_max</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="n" style="color: #333;">yaxis</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yRange</span><span class="p">)</span></span>
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_traces</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="python"> <span class="n" style="color: #333;">fig</span><span class="p">[</span><span class="s" style="color: #d14;">'layout'</span><span class="p">][</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annos</span></span>
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="python"> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">out_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">auto_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +41,7 @@ def convertCmap(c, vmin=0, vmax=1):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">254</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">colorScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">255</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint8</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">cmap</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">h</span><span class="p">)[:</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">255</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint8</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">cmap</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">h</span><span class="p">)[:</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">255</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">colorScale</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="s" style="color: #d14;">'rgb'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">((</span><span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">C</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))])</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">colorScale</span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#abc059e39dfccf4038fabfb18bfb7b5121e4e2e4"><strong>galaxy/wrapper/computeMatrixOperations.xml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,6 +74,7 @@</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="xml"> #else if $submodule.command == "dataRange":</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="xml"> dataRange</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="xml"> -m $submodule.matrixFile</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="xml"> > $outFileTxt</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="xml"> #end if</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="xml">]]></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="xml"> <span class="nt" style="color: #000080;"></command></span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="xml"> <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"dataRange"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="xml"> <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">argument=</span><span class="s" style="color: #d14;">"matrixFile"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"deeptools_compute_matrix_archive"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="xml"> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Matrix file from the computeMatrix tool"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="xml"> <span class="nt" style="color: #000080;"></param></span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="xml"> <span class="nt" style="color: #000080;"></when></span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="xml"> <span class="nt" style="color: #000080;"></conditional></span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="xml"> <span class="nt" style="color: #000080;"></inputs></span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#d2de9c6869fd65911899bace5f34a175e96efb2a"><strong>galaxy/wrapper/deepTools_macros.xml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="nt" style="color: #000080;"><macros></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@THREADS@"</span><span class="nt" style="color: #000080;">></span>--numberOfProcessors "\${GALAXY_SLOTS:-4}"<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.5.<span class="idiff left right">0</span>.0<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml"> <span class="nt" style="color: #000080;"><token</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"@WRAPPER_VERSION@"</span><span class="nt" style="color: #000080;">></span>3.5.<span class="idiff left right">1</span>.0<span class="nt" style="color: #000080;"></token></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xml</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"requirements"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirements></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.5.<span class="idiff left right">0</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.5.<span class="idiff left right">1</span>"</span><span class="nt" style="color: #000080;">></span>deeptools<span class="nt" style="color: #000080;"></requirement></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"> <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"1.9"</span><span class="nt" style="color: #000080;">></span>samtools<span class="nt" style="color: #000080;"></requirement></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"> <span class="nt" style="color: #000080;"></requirements></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"> <span class="nt" style="color: #000080;"><expand</span> <span class="na" style="color: #008080;">macro=</span><span class="s" style="color: #d14;">"stdio"</span> <span class="nt" style="color: #000080;">/></span></span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#5bb35761036ed12cc2d6fc54c2928bcdfd2e5071"><strong>galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Median: 242.0</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Max.: 251.0</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Std: 4.496912521077347</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">MAD: 1.0</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Len. 10%: 241.2<span class="idiff left right">0000000000002</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Len. 10%: 241.2</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Len. 20%: 241.4</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Len. 30%: 241.6</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Len. 40%: 241.8</span>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#a5d8ab9e3ca6b3aabfc033e525b08b190362aa98"><strong>galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"> Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99%</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.2<span class="idiff left right">0000000000002</span> 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.2 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0</span></pre>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#0fe7a0a47ac88c595cb77d4fe718abef6e1d4b88"><strong>galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 <span class="idiff left">NA</span> 0.2690044980681214<span class="idiff right">3 NA NA NA</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.2690044980681214<span class="idiff left right">3</span> 0 0 0</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 <span class="idiff left">nan</span> 0.2690044980681214<span class="idiff right"> nan nan nan</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.2690044980681214 0 0 0</span></pre>
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<a href="https://salsa.debian.org/med-team/python-deeptools/-/commit/efaae4b3880dac7d7f0b2d4cd8a11618e10afccf#e775e2873f0a3295f76cd404ea49d1531c224470"><strong>galaxy/wrapper/test-data/plotPCA_result2.tabular</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#plotPCA --outFileNameData</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">1 -0.7071067811865476 -0.7071067811865475 4.0</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">2 -0.7071067811865475 0.7071067811865476 <span class="idiff left right">1.2325951644078315</span>e-32</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">2 -0.7071067811865475 0.7071067811865476 <span class="idiff left right">2.49319462166397</span>e-32</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/numpy" rel="nofollow noreferrer noopener" target="_blank">numpy</a>>=1.9.0</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/scipy" rel="nofollow noreferrer noopener" target="_blank">scipy</a>>=0.17.0</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/matplotlib" rel="nofollow noreferrer noopener" target="_blank">matplotlib</a>>=3.<span class="idiff left right">1</span>.0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/matplotlib" rel="nofollow noreferrer noopener" target="_blank">matplotlib</a>>=3.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pysam" rel="nofollow noreferrer noopener" target="_blank">pysam</a>>=0.14.0</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/py2bit" rel="nofollow noreferrer noopener" target="_blank">py2bit</a>>=0.2.0</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/numpydoc" rel="nofollow noreferrer noopener" target="_blank">numpydoc</a>>=0.5</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyBigWig" rel="nofollow noreferrer noopener" target="_blank">pyBigWig</a>>=0.2.1</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/plotly" rel="nofollow noreferrer noopener" target="_blank">plotly</a>>=<span class="idiff left right">2.0.0</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/plotly" rel="nofollow noreferrer noopener" target="_blank">plotly</a>>=<span class="idiff left right">4.9</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/deeptoolsintervals" rel="nofollow noreferrer noopener" target="_blank">deeptoolsintervals</a>>=0.1.8</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,12 +84,12 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"numpy >= 1.9.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"scipy >= 0.17.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"matplotlib >= 3.<span class="idiff left right">1</span>.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"matplotlib >= 3.<span class="idiff left right">3</span>.0"</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"pysam >= 0.14.0"</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"numpydoc >= 0.5"</span><span class="p">,</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"pyBigWig >= 0.2.1"</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"py2bit >= 0.2.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"plotly >= <span class="idiff left right">2.0.0</span>"</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"plotly >= <span class="idiff left right">4.9</span>"</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">"deeptoolsintervals >= 0.1.8"</span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="p">],</span></span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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