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Zhuoqing Fang committed Dec 11, 2017
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2 changes: 1 addition & 1 deletion docs/_build/html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: c5f7ae6eaa5bd145b0d64942d289bd4a
config: 5f64865c08445ce1ddd56988930b40b0
tags: 645f666f9bcd5a90fca523b33c5a78b7
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83 changes: 39 additions & 44 deletions docs/_build/html/_modules/gseapy/algorithm.html
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8 changes: 4 additions & 4 deletions docs/_build/html/_modules/gseapy/enrichr.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>gseapy.enrichr &mdash; GSEApy 0.8.9 documentation</title>
<title>gseapy.enrichr &mdash; GSEApy 0.9.0 documentation</title>



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<link rel="index" title="Index"
href="../../genindex.html"/>
<link rel="search" title="Search" href="../../search.html"/>
<link rel="top" title="GSEApy 0.8.9 documentation" href="../../index.html"/>
<link rel="top" title="GSEApy 0.9.0 documentation" href="../../index.html"/>
<link rel="up" title="Module code" href="../index.html"/>


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<div class="version">
0.8.9
0.9.0
</div>


Expand Down Expand Up @@ -375,7 +375,7 @@ <h1>Source code for gseapy.enrichr</h1><div class="highlight"><pre>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'../../',
VERSION:'0.8.9',
VERSION:'0.9.0',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
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80 changes: 55 additions & 25 deletions docs/_build/html/_modules/gseapy/gsea.html
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8 changes: 4 additions & 4 deletions docs/_build/html/_modules/gseapy/parser.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>gseapy.parser &mdash; GSEApy 0.8.9 documentation</title>
<title>gseapy.parser &mdash; GSEApy 0.9.0 documentation</title>



Expand All @@ -35,7 +35,7 @@
<link rel="index" title="Index"
href="../../genindex.html"/>
<link rel="search" title="Search" href="../../search.html"/>
<link rel="top" title="GSEApy 0.8.9 documentation" href="../../index.html"/>
<link rel="top" title="GSEApy 0.9.0 documentation" href="../../index.html"/>
<link rel="up" title="Module code" href="../index.html"/>


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<div class="version">
0.8.9
0.9.0
</div>


Expand Down Expand Up @@ -377,7 +377,7 @@ <h1>Source code for gseapy.parser</h1><div class="highlight"><pre>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'../../',
VERSION:'0.8.9',
VERSION:'0.9.0',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
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14 changes: 8 additions & 6 deletions docs/_build/html/_modules/gseapy/plot.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>gseapy.plot &mdash; GSEApy 0.8.9 documentation</title>
<title>gseapy.plot &mdash; GSEApy 0.9.0 documentation</title>



Expand All @@ -35,7 +35,7 @@
<link rel="index" title="Index"
href="../../genindex.html"/>
<link rel="search" title="Search" href="../../search.html"/>
<link rel="top" title="GSEApy 0.8.9 documentation" href="../../index.html"/>
<link rel="top" title="GSEApy 0.9.0 documentation" href="../../index.html"/>
<link rel="up" title="Module code" href="../index.html"/>


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<div class="version">
0.8.9
0.9.0
</div>


Expand Down Expand Up @@ -287,6 +287,8 @@ <h1>Source code for gseapy.plot</h1><div class="highlight"><pre>
<span class="n">fdr_label</span> <span class="o">=</span> <span class="s1">&#39;FDR: &#39;</span><span class="o">+</span> <span class="s2">&quot;</span><span class="si">{:.3f}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">fdr</span><span class="p">))</span>
<span class="n">im_matrix</span> <span class="o">=</span> <span class="n">rank_metric</span><span class="o">.</span><span class="n">ix</span><span class="p">[:,</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">T</span>

<span class="c1">#output truetype</span>
<span class="n">plt</span><span class="o">.</span><span class="n">rcParams</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;pdf.fonttype&#39;</span><span class="p">:</span><span class="mi">42</span><span class="p">,</span><span class="s1">&#39;ps.fonttype&#39;</span><span class="p">:</span><span class="mi">42</span><span class="p">})</span>
<span class="c1">#in most case, we will have mangy plots, so do not display plots</span>
<span class="c1">#It&#39;s also convinient to run this script on command line.</span>

Expand All @@ -299,8 +301,8 @@ <h1>Source code for gseapy.plot</h1><div class="highlight"><pre>
<span class="n">ax1</span> <span class="o">=</span> <span class="n">fig</span><span class="o">.</span><span class="n">add_subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">11</span><span class="p">:])</span>
<span class="k">if</span> <span class="n">module</span> <span class="o">==</span> <span class="s1">&#39;ssgsea&#39;</span><span class="p">:</span>
<span class="n">nes_label</span> <span class="o">=</span> <span class="s1">&#39;ES: &#39;</span><span class="o">+</span> <span class="s2">&quot;</span><span class="si">{:.3f}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">nes</span><span class="p">))</span>
<span class="n">pval_label</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
<span class="n">fdr_label</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
<span class="n">pval_label</span><span class="o">=</span><span class="s1">&#39;Pval: &#39;</span>
<span class="n">fdr_label</span><span class="o">=</span><span class="s1">&#39;FDR: &#39;</span>
<span class="n">ax1</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y1</span><span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">rank_metric</span><span class="p">[</span><span class="s1">&#39;rank&#39;</span><span class="p">]),</span> <span class="n">y2</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;#C9D3DB&#39;</span><span class="p">)</span>
<span class="n">ax1</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;log ranked metric&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
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<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'../../',
VERSION:'0.8.9',
VERSION:'0.9.0',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
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8 changes: 4 additions & 4 deletions docs/_build/html/_modules/index.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>Overview: module code &mdash; GSEApy 0.8.9 documentation</title>
<title>Overview: module code &mdash; GSEApy 0.9.0 documentation</title>



Expand All @@ -35,7 +35,7 @@
<link rel="index" title="Index"
href="../genindex.html"/>
<link rel="search" title="Search" href="../search.html"/>
<link rel="top" title="GSEApy 0.8.9 documentation" href="../index.html"/>
<link rel="top" title="GSEApy 0.9.0 documentation" href="../index.html"/>


<script src="../_static/js/modernizr.min.js"></script>
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<div class="version">
0.8.9
0.9.0
</div>


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<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'../',
VERSION:'0.8.9',
VERSION:'0.9.0',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
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