AMR/docs/reference/pca.html

373 lines
16 KiB
HTML
Raw Normal View History

2020-03-07 21:48:21 +01:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
2020-03-08 11:18:59 +01:00
<title>Principal Component Analysis (for AMR) — pca • AMR (for R)</title>
2020-03-07 21:48:21 +01:00
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
<!-- jquery -->
2020-04-13 21:09:56 +02:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
2020-03-07 21:48:21 +01:00
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
2020-12-21 22:46:29 +01:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
2020-12-21 22:46:29 +01:00
2020-04-17 19:16:30 +02:00
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
2020-03-07 21:48:21 +01:00
<!-- Font Awesome icons -->
2020-04-17 19:16:30 +02:00
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
2020-03-07 21:48:21 +01:00
<!-- clipboard.js -->
2020-04-17 19:16:30 +02:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
2020-03-07 21:48:21 +01:00
<!-- headroom.js -->
2020-04-17 19:16:30 +02:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
2020-03-07 21:48:21 +01:00
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
2020-03-08 11:18:59 +01:00
<meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
<meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
2020-03-07 21:48:21 +01:00
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
2020-04-17 19:16:30 +02:00
<body data-spy="scroll" data-target="#toc">
2020-03-07 21:48:21 +01:00
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
2020-03-07 21:48:21 +01:00
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-home"></span>
2020-03-07 21:48:21 +01:00
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
2020-12-21 22:46:29 +01:00
<span class="fas fa-question-circle"></span>
2020-03-07 21:48:21 +01:00
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-directions"></span>
2020-03-07 21:48:21 +01:00
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-dice"></span>
2020-03-07 21:48:21 +01:00
Predict antimicrobial resistance
</a>
</li>
2020-08-21 11:40:13 +02:00
<li>
<a href="../articles/datasets.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-database"></span>
2020-08-21 11:40:13 +02:00
Data sets for download / own use
2020-08-21 11:40:13 +02:00
</a>
</li>
2020-03-07 21:48:21 +01:00
<li>
<a href="../articles/PCA.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-compress"></span>
2020-03-07 21:48:21 +01:00
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-skull-crossbones"></span>
2020-03-07 21:48:21 +01:00
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-globe-americas"></span>
2020-03-07 21:48:21 +01:00
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-file-upload"></span>
2020-03-07 21:48:21 +01:00
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-exchange-alt"></span>
2020-03-07 21:48:21 +01:00
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-bug"></span>
2020-03-07 21:48:21 +01:00
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-capsules"></span>
2020-03-07 21:48:21 +01:00
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-shipping-fast"></span>
2020-03-07 21:48:21 +01:00
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../reference/index.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-book-open"></span>
2020-03-07 21:48:21 +01:00
Manual
</a>
</li>
<li>
<a href="../authors.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-users"></span>
2020-03-07 21:48:21 +01:00
Authors
</a>
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../news/index.html">
2020-12-21 22:46:29 +01:00
<span class="far fa-newspaper"></span>
2020-03-07 21:48:21 +01:00
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
2020-07-08 14:48:06 +02:00
<a href="https://github.com/msberends/AMR">
2020-12-21 22:46:29 +01:00
<span class="fab fa-github"></span>
2020-03-07 21:48:21 +01:00
Source Code
</a>
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../survey.html">
2020-12-21 22:46:29 +01:00
<span class="fas fa-clipboard-list"></span>
2020-03-07 21:48:21 +01:00
2020-07-28 18:39:57 +02:00
Survey
2020-03-07 21:48:21 +01:00
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Principal Component Analysis (for AMR)</h1>
2020-07-08 14:48:06 +02:00
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
2020-03-07 21:48:21 +01:00
<div class="hidden name"><code>pca.Rd</code></div>
</div>
<div class="ref-description">
2020-03-08 11:18:59 +01:00
<p>Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.</p>
2020-03-07 21:48:21 +01:00
</div>
2020-10-26 12:23:03 +01:00
<pre class="usage"><span class='fu'>pca</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>...</span>,
retx <span class='op'>=</span> <span class='cn'>TRUE</span>,
center <span class='op'>=</span> <span class='cn'>TRUE</span>,
scale. <span class='op'>=</span> <span class='cn'>TRUE</span>,
tol <span class='op'>=</span> <span class='cn'>NULL</span>,
rank. <span class='op'>=</span> <span class='cn'>NULL</span>
<span class='op'>)</span></pre>
2020-03-07 21:48:21 +01:00
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing numeric columns</p></td>
</tr>
<tr>
<th>...</th>
2020-05-16 13:05:47 +02:00
<td><p>columns of <code>x</code> to be selected for PCA, can be unquoted since it supports quasiquotation.</p></td>
2020-03-07 21:48:21 +01:00
</tr>
<tr>
<th>retx</th>
<td><p>a logical value indicating whether the rotated variables
should be returned.</p></td>
</tr>
<tr>
<th>center</th>
<td><p>a logical value indicating whether the variables
should be shifted to be zero centered. Alternately, a vector of
length equal the number of columns of <code>x</code> can be supplied.
The value is passed to <code>scale</code>.</p></td>
</tr>
<tr>
<th>scale.</th>
<td><p>a logical value indicating whether the variables should
be scaled to have unit variance before the analysis takes
place. The default is <code>FALSE</code> for consistency with S, but
in general scaling is advisable. Alternatively, a vector of length
equal the number of columns of <code>x</code> can be supplied. The
value is passed to <code><a href='https://rdrr.io/r/base/scale.html'>scale</a></code>.</p></td>
</tr>
<tr>
<th>tol</th>
<td><p>a value indicating the magnitude below which components
should be omitted. (Components are omitted if their
standard deviations are less than or equal to <code>tol</code> times the
standard deviation of the first component.) With the default null
setting, no components are omitted (unless <code>rank.</code> is specified
less than <code><a href='https://rdrr.io/r/base/Extremes.html'>min(dim(x))</a></code>.). Other settings for tol could be
<code>tol = 0</code> or <code>tol = sqrt(.Machine$double.eps)</code>, which
would omit essentially constant components.</p></td>
</tr>
<tr>
<th>rank.</th>
<td><p>optionally, a number specifying the maximal rank, i.e.,
maximal number of principal components to be used. Can be set as
alternative or in addition to <code>tol</code>, useful notably when the
desired rank is considerably smaller than the dimensions of the matrix.</p></td>
</tr>
</table>
2020-03-08 11:18:59 +01:00
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An object of classes pca and <a href='https://rdrr.io/r/stats/prcomp.html'>prcomp</a></p>
2020-03-07 21:48:21 +01:00
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
2020-03-08 11:18:59 +01:00
<p>The <code>pca()</code> function takes a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> as input and performs the actual PCA with the <span style="R">R</span> function <code><a href='https://rdrr.io/r/stats/prcomp.html'>prcomp()</a></code>.</p>
<p>The result of the <code>pca()</code> function is a <a href='https://rdrr.io/r/stats/prcomp.html'>prcomp</a> object, with an additional attribute <code>non_numeric_cols</code> which is a vector with the column names of all columns that do not contain numeric values. These are probably the groups and labels, and will be used by <code><a href='ggplot_pca.html'>ggplot_pca()</a></code>.</p>
2020-03-14 14:05:43 +01:00
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
2020-03-07 21:48:21 +01:00
2020-03-14 14:05:43 +01:00
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
2020-07-08 14:48:06 +02:00
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
2020-03-07 21:48:21 +01:00
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># \donttest{</span>
2020-10-26 12:23:03 +01:00
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># calculate the resistance per group first </span>
2020-10-26 12:23:03 +01:00
<span class='va'>resistance_data</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>order <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_order</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span>, <span class='co'># group on anything, like order</span>
genus <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span>, <span class='va'>resistance</span><span class='op'>)</span> <span class='co'># then get resistance of all drugs</span>
<span class='co'># now conduct PCA for certain antimicrobial agents</span>
2020-10-26 12:23:03 +01:00
<span class='va'>pca_result</span> <span class='op'>&lt;-</span> <span class='va'>resistance_data</span> <span class='op'>%&gt;%</span>
<span class='fu'>pca</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>CXM</span>, <span class='va'>CTX</span>, <span class='va'>CAZ</span>, <span class='va'>GEN</span>, <span class='va'>TOB</span>, <span class='va'>TMP</span>, <span class='va'>SXT</span><span class='op'>)</span>
2020-10-26 12:23:03 +01:00
<span class='va'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span> <span class='co'># a new and convenient plot function</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
2020-03-07 21:48:21 +01:00
</div>
2020-04-13 21:09:56 +02:00
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
2020-04-17 19:16:30 +02:00
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
2020-03-07 21:48:21 +01:00
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
2020-03-07 21:48:21 +01:00
</div>
</footer>
</div>
</body>
</html>