AMR/docs/reference/ggplot_rsi.html

533 lines
32 KiB
HTML
Raw Normal View History

2018-12-23 21:26:21 +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">
<title>AMR Plots with ggplot2 — ggplot_rsi • AMR (for R)</title>
2018-12-29 22:24:19 +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" />
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
<!-- 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>
2018-12-23 21:26:21 +01:00
<!-- Bootstrap -->
2020-12-27 00:07:00 +01:00
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
2019-10-13 09:31:58 +02:00
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>
2018-12-23 21:26:21 +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" />
2018-12-23 21:26:21 +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>
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
<!-- 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>
2018-12-23 21:26:21 +01:00
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
2018-12-29 22:24:19 +01:00
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
2018-12-23 21:26:21 +01:00
<meta property="og:title" content="AMR Plots with ggplot2 — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for AMR data analysis. All functions rely on ggplot2 functions." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +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]-->
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
</head>
2020-04-17 19:16:30 +02:00
<body data-spy="scroll" data-target="#toc">
2018-12-23 21:26:21 +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">
2018-12-29 22:24:19 +01:00
<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">1.5.0.9016</span>
2018-12-23 21:26:21 +01:00
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-home"></span>
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Home
2018-12-23 21:26:21 +01:00
</a>
</li>
2019-01-02 23:24:07 +01:00
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
2020-12-17 16:22:25 +01:00
<span class="fas fa-question-circle"></span>
2019-01-02 23:24:07 +01:00
How to
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
<span class="caret"></span>
2018-12-29 22:24:19 +01:00
</a>
2019-01-02 23:24:07 +01:00
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-directions"></span>
2019-01-02 23:24:07 +01:00
Conduct AMR analysis
</a>
</li>
<li>
2019-02-14 10:23:51 +01:00
<a href="../articles/resistance_predict.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-dice"></span>
2019-01-02 23:24:07 +01:00
Predict antimicrobial resistance
</a>
</li>
2020-08-21 11:40:13 +02:00
<li>
<a href="../articles/datasets.html">
2020-12-17 16:22:25 +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>
2020-04-13 21:09:56 +02:00
<li>
<a href="../articles/PCA.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-compress"></span>
2020-04-13 21:09:56 +02:00
Conduct principal component analysis for AMR
</a>
</li>
2019-05-23 16:58:59 +02:00
<li>
<a href="../articles/MDR.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-skull-crossbones"></span>
2019-05-23 16:58:59 +02:00
Determine multi-drug resistance (MDR)
</a>
</li>
2019-01-29 00:06:50 +01:00
<li>
<a href="../articles/WHONET.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-globe-americas"></span>
2019-01-29 00:06:50 +01:00
Work with WHONET data
</a>
</li>
2019-02-14 15:18:17 +01:00
<li>
<a href="../articles/SPSS.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-file-upload"></span>
2019-02-14 15:18:17 +01:00
Import data from SPSS/SAS/Stata
</a>
</li>
2019-01-02 23:24:07 +01:00
<li>
<a href="../articles/EUCAST.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-exchange-alt"></span>
2019-01-02 23:24:07 +01:00
Apply EUCAST rules
</a>
</li>
<li>
2019-02-14 10:23:51 +01:00
<a href="../reference/mo_property.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-bug"></span>
2019-01-02 23:24:07 +01:00
Get properties of a microorganism
</a>
</li>
<li>
2019-05-10 16:44:59 +02:00
<a href="../reference/ab_property.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-capsules"></span>
2019-01-02 23:24:07 +01:00
Get properties of an antibiotic
</a>
</li>
2019-01-11 20:37:23 +01:00
<li>
<a href="../articles/benchmarks.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-shipping-fast"></span>
2019-01-11 20:37:23 +01:00
Other: benchmarks
</a>
</li>
2019-01-02 23:24:07 +01:00
</ul>
2018-12-23 21:26:21 +01:00
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../reference/index.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-book-open"></span>
2018-12-29 22:24:19 +01:00
Manual
</a>
2018-12-23 21:26:21 +01:00
</li>
2018-12-29 22:24:19 +01:00
<li>
<a href="../authors.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-users"></span>
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Authors
2018-12-23 21:26:21 +01:00
</a>
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../news/index.html">
2020-12-17 16:22:25 +01:00
<span class="far fa-newspaper"></span>
2018-12-29 22:24:19 +01:00
Changelog
</a>
</li>
2019-01-02 23:24:07 +01:00
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
2020-07-08 14:48:06 +02:00
<a href="https://github.com/msberends/AMR">
2020-12-17 16:22:25 +01:00
<span class="fab fa-github"></span>
2018-12-29 22:24:19 +01:00
Source Code
</a>
2018-12-23 21:26:21 +01:00
</li>
2019-01-02 23:24:07 +01:00
<li>
2020-07-28 18:39:57 +02:00
<a href="../survey.html">
2020-12-17 16:22:25 +01:00
<span class="fas fa-clipboard-list"></span>
2018-12-29 22:24:19 +01:00
2020-07-28 18:39:57 +02:00
Survey
2018-12-29 22:24:19 +01:00
</a>
</li>
2018-12-23 21:26:21 +01:00
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>AMR Plots with <code>ggplot2</code></h1>
2020-07-08 14:48:06 +02:00
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ggplot_rsi.R'><code>R/ggplot_rsi.R</code></a></small>
2018-12-23 21:26:21 +01:00
<div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to create bar plots for AMR data analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
2018-12-23 21:26:21 +01:00
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
<span class='va'>data</span>,
position <span class='op'>=</span> <span class='cn'>NULL</span>,
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
facet <span class='op'>=</span> <span class='cn'>NULL</span>,
breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>,
limits <span class='op'>=</span> <span class='cn'>NULL</span>,
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
minimum <span class='op'>=</span> <span class='fl'>30</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
nrow <span class='op'>=</span> <span class='cn'>NULL</span>,
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
<span class='st'>"#ff6961"</span><span class='op'>)</span>,
datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>,
2020-10-21 13:07:23 +02:00
datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>,
title <span class='op'>=</span> <span class='cn'>NULL</span>,
subtitle <span class='op'>=</span> <span class='cn'>NULL</span>,
caption <span class='op'>=</span> <span class='cn'>NULL</span>,
x.title <span class='op'>=</span> <span class='st'>"Antimicrobial"</span>,
y.title <span class='op'>=</span> <span class='st'>"Proportion"</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>geom_rsi</span><span class='op'>(</span>
position <span class='op'>=</span> <span class='cn'>NULL</span>,
x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span><span class='op'>)</span>,
fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
minimum <span class='op'>=</span> <span class='fl'>30</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>facet_rsi</span><span class='op'>(</span>facet <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span><span class='op'>)</span>, nrow <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>scale_y_percent</span><span class='op'>(</span>breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>, limits <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span>
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
<span class='st'>"#ff6961"</span><span class='op'>)</span>
<span class='op'>)</span>
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>labels_rsi_count</span><span class='op'>(</span>
position <span class='op'>=</span> <span class='cn'>NULL</span>,
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
minimum <span class='op'>=</span> <span class='fl'>30</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
2020-10-21 13:07:23 +02:00
datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>
<span class='op'>)</span></pre>
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +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>data</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with column(s) of class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>position</th>
<td><p>position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>x</th>
2019-06-13 14:28:46 +02:00
<td><p>variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>fill</th>
2019-06-13 14:28:46 +02:00
<td><p>variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>facet</th>
2019-06-13 14:28:46 +02:00
<td><p>variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>breaks</th>
<td><p>numeric vector of positions</p></td>
</tr>
<tr>
<th>limits</th>
<td><p>numeric vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></td>
</tr>
<tr>
<th>translate_ab</th>
2020-12-17 16:22:25 +01:00
<td><p>a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code></p></td>
2019-05-13 10:10:16 +02:00
</tr>
<tr>
<th>combine_SI</th>
2020-12-22 00:51:17 +01:00
<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
2019-05-13 12:21:57 +02:00
</tr>
<tr>
<th>combine_IR</th>
2020-12-22 00:51:17 +01:00
<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see argument <code>combine_SI</code>.</p></td>
2019-05-10 16:44:59 +02:00
</tr>
<tr>
<th>minimum</th>
<td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></td>
</tr>
2019-05-10 16:44:59 +02:00
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption("AMR_locale")</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>nrow</th>
<td><p>(when using <code>facet</code>) number of rows</p></td>
</tr>
2019-05-31 20:25:57 +02:00
<tr>
<th>colours</th>
2020-11-24 11:47:54 +01:00
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours.</p></td>
2019-05-31 20:25:57 +02:00
</tr>
2018-12-23 21:26:21 +01:00
<tr>
<th>datalabels</th>
<td><p>show datalabels using <code>labels_rsi_count()</code></p></td>
2018-12-23 21:26:21 +01:00
</tr>
<tr>
<th>datalabels.size</th>
<td><p>size of the datalabels</p></td>
</tr>
<tr>
<th>datalabels.colour</th>
<td><p>colour of the datalabels</p></td>
</tr>
2019-05-31 20:25:57 +02:00
<tr>
<th>title</th>
<td><p>text to show as title of the plot</p></td>
</tr>
<tr>
<th>subtitle</th>
<td><p>text to show as subtitle of the plot</p></td>
</tr>
<tr>
<th>caption</th>
<td><p>text to show as caption of the plot</p></td>
</tr>
<tr>
<th>x.title</th>
<td><p>text to show as x axis description</p></td>
</tr>
<tr>
<th>y.title</th>
<td><p>text to show as y axis description</p></td>
</tr>
2018-12-23 21:26:21 +01:00
<tr>
<th>...</th>
2020-12-22 00:51:17 +01:00
<td><p>other arguments passed on to <code>geom_rsi()</code></p></td>
2018-12-23 21:26:21 +01:00
</tr>
</table>
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The Functions</h3>
2019-11-29 19:43:23 +01:00
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
2020-07-08 14:48:06 +02:00
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code><a href='https://ggplot2.tidyverse.org/reference/scale_manual.html'>ggplot2::scale_fill_manual()</a></code>.</p>
<p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>ggplot2::theme()</a></code> with minimal distraction.</p>
2020-07-08 14:48:06 +02:00
<p><code>labels_rsi_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>ggplot2::geom_text()</a></code>.</p>
<p><code>ggplot_rsi()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See <em>Examples</em>.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<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>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
2019-01-02 23:24:07 +01:00
2019-10-13 09:31:58 +02:00
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
2018-12-23 21:26:21 +01:00
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><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='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;</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>
2020-08-10 12:46:03 +02:00
2020-05-16 21:40:50 +02:00
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
2020-05-16 21:40:50 +02:00
<span class='co'># prettify the plot using some additional functions:</span>
<span class='va'>df</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/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>scale_y_percent</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>labels_rsi_count</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
2020-05-16 21:40:50 +02:00
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
2020-05-16 21:40:50 +02:00
<span class='co'># get only proportions and no counts:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
2020-12-22 00:51:17 +01:00
<span class='co'># add other ggplot2 arguments as you like:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>width <span class='op'>=</span> <span class='fl'>0.5</span>,
colour <span class='op'>=</span> <span class='st'>"black"</span>,
size <span class='op'>=</span> <span class='fl'>1</span>,
linetype <span class='op'>=</span> <span class='fl'>2</span>,
alpha <span class='op'>=</span> <span class='fl'>0.25</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>SI <span class='op'>=</span> <span class='st'>"yellow"</span><span class='op'>)</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
<span class='op'>}</span>
2020-08-10 12:46:03 +02:00
<span class='co'># \donttest{</span>
2018-12-23 21:26:21 +01:00
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
<span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2020-11-24 11:47:54 +01:00
<span class='co'># age_groups() is also a function in this AMR package:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
<span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
2020-08-10 12:46:03 +02:00
2018-12-23 21:26:21 +01:00
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span><span class='op'>(</span><span class='op'>)</span>
2019-05-31 20:25:57 +02:00
<span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
2019-01-02 23:24:07 +01:00
2018-12-23 21:26:21 +01:00
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</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><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"hospital_id"</span>,
facet <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
nrow <span class='op'>=</span> <span class='fl'>1</span>,
title <span class='op'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
x.title <span class='op'>=</span> <span class='st'>"Hospital"</span>,
datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
2018-12-23 21:26:21 +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>
2018-12-23 21:26:21 +01:00
</div>
</div>
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
<footer>
<div class="copyright">
2020-01-26 20:38:54 +01:00
<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>
2018-12-23 21:26:21 +01:00
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
2018-12-23 21:26:21 +01:00
</div>
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
</footer>
</div>
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
</body>
</html>
2019-10-13 09:31:58 +02:00