/
biom.table.Table.align_to.html
127 lines (108 loc) · 8.11 KB
/
biom.table.Table.align_to.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
<!DOCTYPE html>
<html lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>biom.table.Table.align_to — biom-format.org</title>
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../../_static/haiku.css?v=dfa0e015" />
<script src="../../_static/documentation_options.js?v=30ffe591"></script>
<script src="../../_static/doctools.js?v=9a2dae69"></script>
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../_static/copybutton.js?v=1d1412a1"></script>
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="biom.table.Table.align_to_dataframe" href="biom.table.Table.align_to_dataframe.html" />
<link rel="prev" title="biom.table.Table.add_metadata" href="biom.table.Table.add_metadata.html" />
</head><body>
<a href="https://github.com/biocore/biom-format"><img
style="position: absolute; top: 0; right: 0; border: 0;"
src="https://s3.amazonaws.com/github/ribbons/forkme_right_red_aa0000.png"
alt="Fork me on GitHub"></a>
<div class="header" role="banner"><h1 class="heading"><a href="../../index.html">
<span>biom-format.org</span></a></h1>
<h2 class="heading"><span>biom.table.Table.align_to</span></h2>
</div>
<div class="topnav" role="navigation" aria-label="top navigation">
<p>
«  <a href="biom.table.Table.add_metadata.html">biom.table.Table.add_metadata</a>
  ::  
<a class="uplink" href="../../index.html">Contents</a>
  ::  
<a href="biom.table.Table.align_to_dataframe.html">biom.table.Table.align_to_dataframe</a>  »
</p>
</div>
<div class="content" role="main">
<section id="biom-table-table-align-to">
<h1>biom.table.Table.align_to<a class="headerlink" href="#biom-table-table-align-to" title="Link to this heading">¶</a></h1>
<dl class="py method">
<dt class="sig sig-object py" id="biom.table.Table.align_to">
<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'detect'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#biom.table.Table.align_to" title="Link to this definition">¶</a></dt>
<dd><p>Align self to other over a requested axis</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><dl class="simple">
<dt><strong>other</strong><span class="classifier">biom.Table</span></dt><dd><p>The table to align too</p>
</dd>
<dt><strong>axis</strong><span class="classifier">str, optional, {sample, observation, both, detect}</span></dt><dd><p>If ‘sample’ or ‘observation’, align to that axis. If ‘both’, align
both axes. If ‘detect’, align what can be aligned.</p>
</dd>
</dl>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><dl class="simple">
<dt>DisjointIDError</dt><dd><p>If the requested axis can’t be aligned.</p>
</dd>
<dt>UnknownAxisError</dt><dd><p>If an unrecognized axis is specified.</p>
</dd>
</dl>
</dd>
</dl>
<p class="rubric">Examples</p>
<p>Align one table to another, for instance a table of 16S data to a table
of metagenomic data. In this example, we’re aligning the samples of the
two tables.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">biom</span> <span class="kn">import</span> <span class="n">Table</span>
<span class="gp">>>> </span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="gp">>>> </span><span class="n">amplicon</span> <span class="o">=</span> <span class="n">Table</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">]]),</span>
<span class="gp">... </span> <span class="p">[</span><span class="s1">'Ecoli'</span><span class="p">,</span> <span class="s1">'Staphylococcus'</span><span class="p">],</span>
<span class="gp">... </span> <span class="p">[</span><span class="s1">'S1'</span><span class="p">,</span> <span class="s1">'S2'</span><span class="p">,</span> <span class="s1">'S3'</span><span class="p">])</span>
<span class="gp">>>> </span><span class="n">metag</span> <span class="o">=</span> <span class="n">Table</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">7</span><span class="p">,</span> <span class="mi">8</span><span class="p">],</span> <span class="p">[</span><span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]]),</span>
<span class="gp">... </span> <span class="p">[</span><span class="s1">'geneA'</span><span class="p">,</span> <span class="s1">'geneB'</span><span class="p">],</span>
<span class="gp">... </span> <span class="p">[</span><span class="s1">'S3'</span><span class="p">,</span> <span class="s1">'S2'</span><span class="p">,</span> <span class="s1">'S1'</span><span class="p">])</span>
<span class="gp">>>> </span><span class="n">amplicon</span> <span class="o">=</span> <span class="n">amplicon</span><span class="o">.</span><span class="n">align_to</span><span class="p">(</span><span class="n">metag</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">amplicon</span><span class="p">)</span>
<span class="go"># Constructed from biom file</span>
<span class="go">#OTU ID S3 S2 S1</span>
<span class="go">Ecoli 2.0 1.0 0.0</span>
<span class="go">Staphylococcus 5.0 4.0 3.0</span>
</pre></div>
</div>
</dd></dl>
</section>
</div>
<div class="bottomnav" role="navigation" aria-label="bottom navigation">
<p>
«  <a href="biom.table.Table.add_metadata.html">biom.table.Table.add_metadata</a>
  ::  
<a class="uplink" href="../../index.html">Contents</a>
  ::  
<a href="biom.table.Table.align_to_dataframe.html">biom.table.Table.align_to_dataframe</a>  »
</p>
</div>
<div class="footer" role="contentinfo">
© Copyright 2011-2024 The BIOM Format Development Team.
Last updated on May 11, 2024.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
</div>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-6636235-6']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>