/
emperor.core.Emperor.html
230 lines (198 loc) · 12.4 KB
/
emperor.core.Emperor.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>emperor.core.Emperor — Emperor 0.9.60 documentation</title>
<link rel="stylesheet" href="../_static/basic.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/style.css" type="text/css" />
<link rel="stylesheet" href="../_static/bootswatch-3.2.0/yeti/bootstrap.min.css" type="text/css" />
<link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
VERSION: '0.9.60',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/copybutton.js"></script>
<script type="text/javascript" src="../_static/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="../_static/js/jquery-fix.js"></script>
<script type="text/javascript" src="../_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
<script type="text/javascript" src="../_static/bootstrap-sphinx.js"></script>
<link rel="top" title="Emperor 0.9.60 documentation" href="../index.html" />
<link rel="up" title="Emperor 3D PCoA viewer (emperor.core)" href="../emperor_objects.html" />
<link rel="next" title="File Formats" href="../formats.html" />
<link rel="prev" title="Emperor 3D PCoA viewer (emperor.core)" href="../emperor_objects.html" />
<meta charset='utf-8'>
<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
<meta name="apple-mobile-web-app-capable" content="yes">
</head>
<body role="document">
<a href="https://github.com/biocore/emperor"
class="visible-desktop hidden-xs"><img
id="gh-banner"
style="position: absolute; top: 50px; right: 0; border: 0;"
src="https://s3.amazonaws.com/github/ribbons/forkme_right_orange_ff7600.png"
alt="Fork me on GitHub"></a>
<script>
// Adjust banner height.
$(function () {
var navHeight = $(".navbar .container").css("height");
$("#gh-banner").css("top", navHeight);
});
</script>
<div id="navbar" class="navbar navbar-default navbar-fixed-top">
<div class="container">
<div class="navbar-header">
<!-- .btn-navbar is used as the toggle for collapsed navbar content -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="../index.html">
Emperor</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.60</b></span>
</div>
<div class="collapse navbar-collapse nav-collapse">
<ul class="nav navbar-nav">
<li class="dropdown globaltoc-container">
<a role="button"
id="dLabelGlobalToc"
data-toggle="dropdown"
data-target="#"
href="../index.html">Site <b class="caret"></b></a>
<ul class="dropdown-menu globaltoc"
role="menu"
aria-labelledby="dLabelGlobalToc"><ul>
<li class="toctree-l1"><a class="reference internal" href="../tutorials/animations.html">Creating an animation using Emperor</a></li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../scripts/make_emperor.html"><em>make_emperor.py</em> – Create three dimensional PCoA plots</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorials/animations.html">Creating an animation using Emperor</a></li>
</ul>
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal" href="../emperor_objects.html">Emperor 3D PCoA viewer (<code class="docutils literal"><span class="pre">emperor.core</span></code>)</a></li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../formats.html">File Formats</a></li>
</ul>
</ul>
</li>
<li class="dropdown">
<a role="button"
id="dLabelLocalToc"
data-toggle="dropdown"
data-target="#"
href="#">Page <b class="caret"></b></a>
<ul class="dropdown-menu localtoc"
role="menu"
aria-labelledby="dLabelLocalToc"><ul>
<li><a class="reference internal" href="#">emperor.core.Emperor</a></li>
</ul>
</ul>
</li>
</ul>
<form class="navbar-form navbar-right" action="../search.html" method="get">
<div class="form-group">
<input type="text" name="q" class="form-control" placeholder="Search" />
</div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="col-md-12">
<div class="section" id="emperor-core-emperor">
<h1>emperor.core.Emperor<a class="headerlink" href="#emperor-core-emperor" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="emperor.core.Emperor">
<em class="property">class </em><code class="descclassname">emperor.core.</code><code class="descname">Emperor</code><span class="sig-paren">(</span><em>ordination</em>, <em>mapping_file_data</em>, <em>mapping_file_headers</em><span class="sig-paren">)</span><a class="headerlink" href="#emperor.core.Emperor" title="Permalink to this definition">¶</a></dt>
<dd><p>Display principal coordinates analysis plots</p>
<p>Use this object to interactively display a PCoA plot using the Emperor
GUI. IPython provides a rich display system that will let you display a
plot inline, without the need of creating a temprorary file or having to
write to disk.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><p class="first"><strong>ordination: skbio.maths.stats.ordination.OrdinationResults</strong></p>
<blockquote>
<div><p>Object containing the computed values for an ordination method in
scikit-bio.</p>
</div></blockquote>
<p><strong>mapping_file_data: list of list objects</strong></p>
<blockquote>
<div><p>Metadata mapping file used to color the plot.</p>
</div></blockquote>
<p><strong>mapping_file_headers: list of str objects</strong></p>
<blockquote class="last">
<div><p>List of strings representing the header names of the
<cite>mapping_file_data</cite>. All names should be unique.</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
<p class="rubric">Notes</p>
<p>This object currently does not support the full range of actions that the
GUI does support and should be considered experimental at the moment.</p>
<p class="rubric">References</p>
<table class="docutils citation" frame="void" id="r2" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id1">[R2]</a></td><td>EMPeror: a tool for visualizing high-throughput microbial community
data Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. Gigascience.
2013 Nov 26;2(1):16.</td></tr>
</tbody>
</table>
<p class="rubric">Examples</p>
<p>Create an Emperor object and display it from the IPython notebook:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">data</span> <span class="o">=</span> <span class="p">[[</span><span class="s1">'PC.354'</span><span class="p">,</span> <span class="s1">'Control'</span><span class="p">,</span> <span class="s1">'20061218'</span><span class="p">,</span> <span class="s1">'Control_mouse_I.D._354'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.355'</span><span class="p">,</span> <span class="s1">'Control'</span><span class="p">,</span> <span class="s1">'20061218'</span><span class="p">,</span> <span class="s1">'Control_mouse_I.D._355'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.356'</span><span class="p">,</span> <span class="s1">'Control'</span><span class="p">,</span> <span class="s1">'20061126'</span><span class="p">,</span> <span class="s1">'Control_mouse_I.D._356'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.481'</span><span class="p">,</span> <span class="s1">'Control'</span><span class="p">,</span> <span class="s1">'20070314'</span><span class="p">,</span> <span class="s1">'Control_mouse_I.D._481'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.593'</span><span class="p">,</span> <span class="s1">'Control'</span><span class="p">,</span> <span class="s1">'20071210'</span><span class="p">,</span> <span class="s1">'Control_mouse_I.D._593'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.607'</span><span class="p">,</span> <span class="s1">'Fast'</span><span class="p">,</span> <span class="s1">'20071112'</span><span class="p">,</span> <span class="s1">'Fasting_mouse_I.D._607'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.634'</span><span class="p">,</span> <span class="s1">'Fast'</span><span class="p">,</span> <span class="s1">'20080116'</span><span class="p">,</span> <span class="s1">'Fasting_mouse_I.D._634'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.635'</span><span class="p">,</span> <span class="s1">'Fast'</span><span class="p">,</span> <span class="s1">'20080116'</span><span class="p">,</span> <span class="s1">'Fasting_mouse_I.D._635'</span><span class="p">],</span>
<span class="gp">... </span><span class="p">[</span><span class="s1">'PC.636'</span><span class="p">,</span> <span class="s1">'Fast'</span><span class="p">,</span> <span class="s1">'20080116'</span><span class="p">,</span> <span class="s1">'Fasting_mouse_I.D._636'</span><span class="p">]]</span>
<span class="gp">>>> </span><span class="n">headers</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'SampleID'</span><span class="p">,</span> <span class="s1">'Treatment'</span><span class="p">,</span> <span class="s1">'DOB'</span><span class="p">,</span> <span class="s1">'Description'</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">ordination</span> <span class="o">=</span> <span class="n">OrdinationResults</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s1">'unweighted_unifrac_pc.txt'</span><span class="p">)</span>
</pre></div>
</div>
<p>Now import the Emperor object and display it using IPython, note that this
call will have no effect under an interactive Python session:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">emperor</span> <span class="k">import</span> <span class="n">Emperor</span>
<span class="gp">>>> </span><span class="n">Emperor</span><span class="p">(</span><span class="n">ordination</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="p">)</span>
</pre></div>
</div>
</dd></dl>
</div>
</div>
</div>
</div>
<footer class="footer">
<div class="container">
<p class="pull-right">
<a href="#">Back to top</a>
</p>
<p>
© Copyright 2014, Emperor Development Team.<br/>
Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.4.<br/>
</p>
</div>
</footer>
</body>
</html>