mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
207 lines
22 KiB
HTML
207 lines
22 KiB
HTML
<!DOCTYPE html>
|
||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Principal Component Analysis (for AMR) — pca • AMR (for R)</title><!-- 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Principal Component Analysis (for AMR) — pca"><meta name="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: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.svg"></head><body>
|
||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||
|
||
|
||
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
|
||
|
||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||
|
||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9083</small>
|
||
|
||
|
||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||
<span class="navbar-toggler-icon"></span>
|
||
</button>
|
||
|
||
<div id="navbar" class="collapse navbar-collapse ms-3">
|
||
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
|
||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
||
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
||
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
||
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
||
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
||
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
||
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
||
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
||
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
||
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
||
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
||
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
||
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
||
</ul></li>
|
||
<li class="nav-item dropdown">
|
||
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
|
||
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & dplyr/tidyverse</a></li>
|
||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & data.table</a></li>
|
||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & tidymodels</a></li>
|
||
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR & base R</a></li>
|
||
</ul></li>
|
||
<li class="active nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
|
||
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
|
||
</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
|
||
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
|
||
</ul></div>
|
||
|
||
|
||
</div>
|
||
</nav><div class="container template-reference-topic">
|
||
<div class="row">
|
||
<main id="main" class="col-md-9"><div class="page-header">
|
||
<img src="../logo.svg" class="logo" alt=""><h1>Principal Component Analysis (for AMR)</h1>
|
||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/pca.R" class="external-link"><code>R/pca.R</code></a></small>
|
||
<div class="d-none name"><code>pca.Rd</code></div>
|
||
</div>
|
||
|
||
<div class="ref-description section level2">
|
||
<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>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pca</span><span class="op">(</span></span>
|
||
<span> <span class="va">x</span>,</span>
|
||
<span> <span class="va">...</span>,</span>
|
||
<span> retx <span class="op">=</span> <span class="cn">TRUE</span>,</span>
|
||
<span> center <span class="op">=</span> <span class="cn">TRUE</span>,</span>
|
||
<span> scale. <span class="op">=</span> <span class="cn">TRUE</span>,</span>
|
||
<span> tol <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||
<span> rank. <span class="op">=</span> <span class="cn">NULL</span></span>
|
||
<span><span class="op">)</span></span></code></pre></div>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||
|
||
|
||
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> columns</p></dd>
|
||
|
||
|
||
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||
<dd><p>columns of <code>x</code> to be selected for PCA, can be unquoted since it supports quasiquotation.</p></dd>
|
||
|
||
|
||
<dt id="arg-retx">retx<a class="anchor" aria-label="anchor" href="#arg-retx"></a></dt>
|
||
<dd><p>a logical value indicating whether the rotated variables
|
||
should be returned.</p></dd>
|
||
|
||
|
||
<dt id="arg-center">center<a class="anchor" aria-label="anchor" href="#arg-center"></a></dt>
|
||
<dd><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></dd>
|
||
|
||
|
||
<dt id="arg-scale-">scale.<a class="anchor" aria-label="anchor" href="#arg-scale-"></a></dt>
|
||
<dd><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" class="external-link">scale</a></code>.</p></dd>
|
||
|
||
|
||
<dt id="arg-tol">tol<a class="anchor" aria-label="anchor" href="#arg-tol"></a></dt>
|
||
<dd><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>min(dim(x))</code>.). Other settings for <code>tol</code> could be
|
||
<code>tol = 0</code> or <code>tol = sqrt(.Machine$double.eps)</code>, which
|
||
would omit essentially constant components.</p></dd>
|
||
|
||
|
||
<dt id="arg-rank-">rank.<a class="anchor" aria-label="anchor" href="#arg-rank-"></a></dt>
|
||
<dd><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></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||
<p>An object of classes pca and <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp</a></p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p>The <code>pca()</code> function takes a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">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" class="external-link">prcomp()</a></code>.</p>
|
||
<p>The result of the <code>pca()</code> function is a <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">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 <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values. These are probably the groups and labels, and will be used by <code><a href="ggplot_pca.html">ggplot_pca()</a></code>.</p>
|
||
</div>
|
||
|
||
<div class="section level2">
|
||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
|
||
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># calculate the resistance per group first</span></span></span>
|
||
<span class="r-in"><span> <span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><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></span></span>
|
||
<span class="r-in"><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></span>
|
||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.sir</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># now conduct PCA for certain antimicrobial drugs</span></span></span>
|
||
<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><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></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="va">pca_result</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># old base R plotting method:</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
|
||
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><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></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><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="op">+</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Title here"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> only_all_tested = FALSE) ...`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` and `genus = "Enterococcus"`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> "TMP", and "TOB". Total observations available: 7.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Groups (n=4, named as 'order'):</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-plt img"><img src="pca-1.png" alt="" width="700" height="433"></span>
|
||
<span class="r-plt img"><img src="pca-2.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
|
||
</footer></div>
|
||
|
||
|
||
|
||
|
||
|
||
</body></html>
|
||
|