mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 21:26:12 +01:00
356 lines
28 KiB
HTML
356 lines
28 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/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||
<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><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><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">
|
||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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><!-- 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="AMR">
|
||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
|
||
<meta name="twitter:card" content="summary_large_image">
|
||
<meta name="twitter:creator" content="@msberends">
|
||
<meta name="twitter:site" content="@univgroningen">
|
||
<!-- 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 data-spy="scroll" data-target="#toc">
|
||
|
||
|
||
<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="Released version">1.7.1.9062</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/datasets.html">
|
||
<span class="fa fa-database"></span>
|
||
|
||
Data sets for download / own use
|
||
</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/index.html">
|
||
<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/index.html">
|
||
<span class="far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://github.com/msberends/AMR" class="external-link">
|
||
<span class="fab fa-github"></span>
|
||
|
||
Source Code
|
||
</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 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||
|
||
|
||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
|
||
<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 class="section level1">
|
||
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||
</h1>
|
||
</div>
|
||
<div class="section level1">
|
||
<h1 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
|
||
</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="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||
<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||
<span class="co"># Rows: 2,000</span>
|
||
<span class="co"># Columns: 49</span>
|
||
<span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
|
||
<span class="co"># $ hospital_id <span style="color: #949494; font-style: italic;"><fct></span> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …</span>
|
||
<span class="co"># $ ward_icu <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…</span>
|
||
<span class="co"># $ ward_clinical <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…</span>
|
||
<span class="co"># $ ward_outpatient <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…</span>
|
||
<span class="co"># $ age <span style="color: #949494; font-style: italic;"><dbl></span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…</span>
|
||
<span class="co"># $ gender <span style="color: #949494; font-style: italic;"><chr></span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…</span>
|
||
<span class="co"># $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "A77334", "A77334", "067927", "067927", "067927", "067…</span>
|
||
<span class="co"># $ mo <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…</span>
|
||
<span class="co"># $ PEN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …</span>
|
||
<span class="co"># $ OXA <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ FLC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …</span>
|
||
<span class="co"># $ AMX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||
<span class="co"># $ AMC <span style="color: #949494; font-style: italic;"><rsi></span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …</span>
|
||
<span class="co"># $ AMP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||
<span class="co"># $ TZP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ CZO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ FEP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ CXM <span style="color: #949494; font-style: italic;"><rsi></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…</span>
|
||
<span class="co"># $ FOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ CTX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||
<span class="co"># $ CAZ <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…</span>
|
||
<span class="co"># $ CRO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||
<span class="co"># $ GEN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ TOB <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…</span>
|
||
<span class="co"># $ AMK <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ KAN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ TMP <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…</span>
|
||
<span class="co"># $ SXT <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …</span>
|
||
<span class="co"># $ NIT <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ FOS <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ LNZ <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||
<span class="co"># $ CIP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …</span>
|
||
<span class="co"># $ MFX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ VAN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…</span>
|
||
<span class="co"># $ TEC <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||
<span class="co"># $ TCY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…</span>
|
||
<span class="co"># $ TGC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||
<span class="co"># $ DOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||
<span class="co"># $ ERY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||
<span class="co"># $ CLI <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …</span>
|
||
<span class="co"># $ AZM <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||
<span class="co"># $ IPM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||
<span class="co"># $ MEM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ MTR <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ CHL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ COL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span>
|
||
<span class="co"># $ MUP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||
<span class="co"># $ RIF <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</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="downlit sourceCode r">
|
||
<code class="sourceCode R"><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 class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/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="../reference/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"><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 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.rsi</span>, <span class="va">resistance</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"># then get resistance of all drugs</span>
|
||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</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 class="co"># and select only relevant columns</span>
|
||
|
||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
|
||
<span class="co"># <span style="color: #949494;"># A tibble: 6 × 10</span></span>
|
||
<span class="co"># <span style="color: #949494;"># Groups: order [5]</span></span>
|
||
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
|
||
<span class="co"># <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">1</span> (unknown order) (unknown ge… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">2</span> Actinomycetales Schaalia <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">3</span> Bacteroidales Bacteroides <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">4</span> Campylobacterales Campylobact… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||
<span class="co"># <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level1">
|
||
<h1 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||
</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="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="va">pca_result</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
|
||
<span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
|
||
<span class="co"># and "TOB". Total observations available: 7.</span></code></pre></div>
|
||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><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 class="co"># Groups (n=4, named as 'order'):</span>
|
||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span>
|
||
<span class="co"># Importance of components:</span>
|
||
<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
|
||
<span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span>
|
||
<span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span>
|
||
<span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
|
||
<pre><code><span class="co"># Groups (n=4, named as 'order'):</span>
|
||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></code></pre>
|
||
<p>Good news. The first two components explain a total of 93.3% 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" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||
</div>
|
||
<div class="section level1">
|
||
<h1 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||
</h1>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><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></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 our 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="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</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="cb8"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span>, ellipse <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">+</span>
|
||
<span class="fu">ggplot2</span><span class="fu">::</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">"An AMR/PCA biplot!"</span><span class="op">)</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="pkgdown-sidebar">
|
||
|
||
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
|
||
</nav>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="copyright">
|
||
<p></p>
|
||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p></p>
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|