mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 06:46:12 +01:00
346 lines
25 KiB
HTML
346 lines
25 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=1.0">
|
||
<title>How to conduct principal component analysis (PCA) for AMR • 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">
|
||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous">
|
||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous">
|
||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
|
||
<script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
|
||
<meta property="og:description" content="">
|
||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
|
||
<meta name="twitter:card" content="summary">
|
||
<!-- 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>
|
||
<body>
|
||
<div class="container template-article">
|
||
<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">1.0.1.9004</span>
|
||
</span>
|
||
</div>
|
||
|
||
<div id="navbar" class="navbar-collapse collapse">
|
||
<ul class="nav navbar-nav">
|
||
<li>
|
||
<a href="../index.html">
|
||
<span class="fa fa-home"></span>
|
||
|
||
Home
|
||
</a>
|
||
</li>
|
||
<li class="dropdown">
|
||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||
<span class="fa fa-question-circle"></span>
|
||
|
||
How to
|
||
|
||
<span class="caret"></span>
|
||
</a>
|
||
<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="../articles/AMR.html">
|
||
<span class="fa fa-directions"></span>
|
||
|
||
Conduct AMR analysis
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/resistance_predict.html">
|
||
<span class="fa fa-dice"></span>
|
||
|
||
Predict antimicrobial resistance
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/PCA.html">
|
||
<span class="fa fa-compress"></span>
|
||
|
||
Conduct principal component analysis for AMR
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/MDR.html">
|
||
<span class="fa fa-skull-crossbones"></span>
|
||
|
||
Determine multi-drug resistance (MDR)
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/WHONET.html">
|
||
<span class="fa fa-globe-americas"></span>
|
||
|
||
Work with WHONET data
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/SPSS.html">
|
||
<span class="fa fa-file-upload"></span>
|
||
|
||
Import data from SPSS/SAS/Stata
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/EUCAST.html">
|
||
<span class="fa fa-exchange-alt"></span>
|
||
|
||
Apply EUCAST rules
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/mo_property.html">
|
||
<span class="fa fa-bug"></span>
|
||
|
||
Get properties of a microorganism
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/ab_property.html">
|
||
<span class="fa fa-capsules"></span>
|
||
|
||
Get properties of an antibiotic
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/benchmarks.html">
|
||
<span class="fa fa-shipping-fast"></span>
|
||
|
||
Other: benchmarks
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/">
|
||
<span class="fa fa-book-open"></span>
|
||
|
||
Manual
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../authors.html">
|
||
<span class="fa fa-users"></span>
|
||
|
||
Authors
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../news/">
|
||
<span class="far fa far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://gitlab.com/msberends/AMR">
|
||
<span class="fab fa fab fa-gitlab"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../LICENSE-text.html">
|
||
<span class="fa fa-book"></span>
|
||
|
||
Licence
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<!--/.nav-collapse -->
|
||
</div>
|
||
<!--/.container -->
|
||
</div>
|
||
<!--/.navbar -->
|
||
|
||
|
||
|
||
</header><div class="row">
|
||
<div class="col-md-9 contents">
|
||
<div class="page-header toc-ignore">
|
||
<h1>How to conduct principal component analysis (PCA) for AMR</h1>
|
||
<h4 class="author">Matthijs S. Berends</h4>
|
||
|
||
<h4 class="date">14 March 2020</h4>
|
||
|
||
|
||
<div class="hidden name"><code>PCA.Rmd</code></div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
|
||
<div id="introduction" class="section level1">
|
||
<h1 class="hasAnchor">
|
||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||
</div>
|
||
<div id="transforming" class="section level1">
|
||
<h1 class="hasAnchor">
|
||
<a href="#transforming" class="anchor"></a>Transforming</h1>
|
||
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
|
||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR)</span>
|
||
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
|
||
<span id="cb1-3"><a href="#cb1-3"></a><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">glimpse</a></span>(example_isolates)</span>
|
||
<span id="cb1-4"><a href="#cb1-4"></a><span class="co"># Observations: 2,000</span></span>
|
||
<span id="cb1-5"><a href="#cb1-5"></a><span class="co"># Variables: 49</span></span>
|
||
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span></span>
|
||
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…</span></span>
|
||
<span id="cb1-8"><a href="#cb1-8"></a><span class="co"># $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…</span></span>
|
||
<span id="cb1-9"><a href="#cb1-9"></a><span class="co"># $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…</span></span>
|
||
<span id="cb1-10"><a href="#cb1-10"></a><span class="co"># $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…</span></span>
|
||
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span></span>
|
||
<span id="cb1-12"><a href="#cb1-12"></a><span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span></span>
|
||
<span id="cb1-13"><a href="#cb1-13"></a><span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span></span>
|
||
<span id="cb1-14"><a href="#cb1-14"></a><span class="co"># $ mo <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…</span></span>
|
||
<span id="cb1-15"><a href="#cb1-15"></a><span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span></span>
|
||
<span id="cb1-16"><a href="#cb1-16"></a><span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-17"><a href="#cb1-17"></a><span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span></span>
|
||
<span id="cb1-18"><a href="#cb1-18"></a><span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-19"><a href="#cb1-19"></a><span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span></span>
|
||
<span id="cb1-20"><a href="#cb1-20"></a><span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-21"><a href="#cb1-21"></a><span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-22"><a href="#cb1-22"></a><span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-23"><a href="#cb1-23"></a><span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-24"><a href="#cb1-24"></a><span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span></span>
|
||
<span id="cb1-25"><a href="#cb1-25"></a><span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-26"><a href="#cb1-26"></a><span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||
<span id="cb1-27"><a href="#cb1-27"></a><span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span></span>
|
||
<span id="cb1-28"><a href="#cb1-28"></a><span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||
<span id="cb1-29"><a href="#cb1-29"></a><span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-30"><a href="#cb1-30"></a><span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span></span>
|
||
<span id="cb1-31"><a href="#cb1-31"></a><span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-32"><a href="#cb1-32"></a><span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-33"><a href="#cb1-33"></a><span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span></span>
|
||
<span id="cb1-34"><a href="#cb1-34"></a><span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span></span>
|
||
<span id="cb1-35"><a href="#cb1-35"></a><span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-36"><a href="#cb1-36"></a><span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-37"><a href="#cb1-37"></a><span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span>
|
||
<span id="cb1-38"><a href="#cb1-38"></a><span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span></span>
|
||
<span id="cb1-39"><a href="#cb1-39"></a><span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-40"><a href="#cb1-40"></a><span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span></span>
|
||
<span id="cb1-41"><a href="#cb1-41"></a><span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span>
|
||
<span id="cb1-42"><a href="#cb1-42"></a><span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span></span>
|
||
<span id="cb1-43"><a href="#cb1-43"></a><span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-44"><a href="#cb1-44"></a><span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span></span>
|
||
<span id="cb1-45"><a href="#cb1-45"></a><span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span></span>
|
||
<span id="cb1-46"><a href="#cb1-46"></a><span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||
<span id="cb1-47"><a href="#cb1-47"></a><span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span></span>
|
||
<span id="cb1-48"><a href="#cb1-48"></a><span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||
<span id="cb1-49"><a href="#cb1-49"></a><span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-50"><a href="#cb1-50"></a><span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-51"><a href="#cb1-51"></a><span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-52"><a href="#cb1-52"></a><span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span></span>
|
||
<span id="cb1-53"><a href="#cb1-53"></a><span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||
<span id="cb1-54"><a href="#cb1-54"></a><span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span></code></pre></div>
|
||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>resistance_data <-<span class="st"> </span>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||
<span id="cb2-2"><a href="#cb2-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">order =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(mo), <span class="co"># group on anything, like order</span></span>
|
||
<span id="cb2-3"><a href="#cb2-3"></a> <span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span><span class="co"># and genus as we do here</span></span>
|
||
<span id="cb2-4"><a href="#cb2-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(is.rsi, resistance) <span class="op">%>%</span><span class="st"> </span><span class="co"># then get resistance of all drugs</span></span>
|
||
<span id="cb2-5"><a href="#cb2-5"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(order, genus, AMC, CXM, CTX, </span>
|
||
<span id="cb2-6"><a href="#cb2-6"></a> CAZ, GEN, TOB, TMP, SXT) <span class="co"># and select only relevant columns</span></span>
|
||
<span id="cb2-7"><a href="#cb2-7"></a></span>
|
||
<span id="cb2-8"><a href="#cb2-8"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(resistance_data)</span>
|
||
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># # A tibble: 6 x 10</span></span>
|
||
<span id="cb2-10"><a href="#cb2-10"></a><span class="co"># # Groups: order [2]</span></span>
|
||
<span id="cb2-11"><a href="#cb2-11"></a><span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span></span>
|
||
<span id="cb2-12"><a href="#cb2-12"></a><span class="co"># <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
|
||
<span id="cb2-13"><a href="#cb2-13"></a><span class="co"># 1 (unknown orde… Micrococcoides NA NA NA NA NA NA NA NA</span></span>
|
||
<span id="cb2-14"><a href="#cb2-14"></a><span class="co"># 2 Actinomycetal… Actinomyces NA NA NA NA NA NA NA NA</span></span>
|
||
<span id="cb2-15"><a href="#cb2-15"></a><span class="co"># 3 Actinomycetal… Corynebacterium NA NA NA NA NA NA NA NA</span></span>
|
||
<span id="cb2-16"><a href="#cb2-16"></a><span class="co"># 4 Actinomycetal… Dermabacter NA NA NA NA NA NA NA NA</span></span>
|
||
<span id="cb2-17"><a href="#cb2-17"></a><span class="co"># 5 Actinomycetal… Micrococcus NA NA NA NA NA NA NA NA</span></span>
|
||
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># 6 Actinomycetal… Propionibacter… NA NA NA NA NA NA NA NA</span></span></code></pre></div>
|
||
</div>
|
||
<div id="perform-principal-component-analysis" class="section level1">
|
||
<h1 class="hasAnchor">
|
||
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
|
||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>pca_result <-<span class="st"> </span><span class="kw"><a href="../reference/pca.html">pca</a></span>(resistance_data)</span>
|
||
<span id="cb3-2"><a href="#cb3-2"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.</span></span>
|
||
<span id="cb3-3"><a href="#cb3-3"></a><span class="co"># Total observations available: 7.</span></span></code></pre></div>
|
||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(pca_result)</span>
|
||
<span id="cb4-2"><a href="#cb4-2"></a><span class="co"># Importance of components:</span></span>
|
||
<span id="cb4-3"><a href="#cb4-3"></a><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
|
||
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># Standard deviation 2.1580 1.6783 0.61282 0.33017 0.20150 0.03190 2.123e-16</span></span>
|
||
<span id="cb4-5"><a href="#cb4-5"></a><span class="co"># Proportion of Variance 0.5821 0.3521 0.04694 0.01363 0.00508 0.00013 0.000e+00</span></span>
|
||
<span id="cb4-6"><a href="#cb4-6"></a><span class="co"># Cumulative Proportion 0.5821 0.9342 0.98117 0.99480 0.99987 1.00000 1.000e+00</span></span></code></pre></div>
|
||
<p>Good news. The first two components explain a total of 93.4% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||
</div>
|
||
<div id="plotting-the-results" class="section level1">
|
||
<h1 class="hasAnchor">
|
||
<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
|
||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(pca_result)</span></code></pre></div>
|
||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||
<p>But we can’t see the explanation of the points. Perhaps this works better with the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(pca_result)</span></code></pre></div>
|
||
<p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
|
||
<p>You can also print an ellipse per group, and edit the appearance:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="kw"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(pca_result, <span class="dt">ellipse =</span> <span class="ot">TRUE</span>) <span class="op">+</span></span>
|
||
<span id="cb7-2"><a href="#cb7-2"></a><span class="st"> </span>ggplot2<span class="op">::</span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"An AMR/PCA biplot!"</span>)</span></code></pre></div>
|
||
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||
|
||
<div id="tocnav">
|
||
<h2 class="hasAnchor">
|
||
<a href="#tocnav" class="anchor"></a>Contents</h2>
|
||
<ul class="nav nav-pills nav-stacked">
|
||
<li><a href="#introduction">Introduction</a></li>
|
||
<li><a href="#transforming">Transforming</a></li>
|
||
<li><a href="#perform-principal-component-analysis">Perform principal component analysis</a></li>
|
||
<li><a href="#plotting-the-results">Plotting the results</a></li>
|
||
</ul>
|
||
</div>
|
||
</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> 1.4.1.</p>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|