<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Functions to plot classes rsi, mic and disk, with support for base R and ggplot2."><title>Plotting for Classes rsi, mic and disk — plot • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.2.2/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.4/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js"integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Plotting for Classes rsi, mic and disk — plot"><metaproperty="og:description"content="Functions to plot classes rsi, mic and disk, with support for base R and ggplot2."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@msberends"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><
<p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <spanstyle="R">R</span> and <code>ggplot2</code>.</p>
<span> main <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">x</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> title <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">object</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> main <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">x</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> mo <spanclass="op">=</span><spanclass="cn">NULL</span>,</span>
<span> ab <spanclass="op">=</span><spanclass="cn">NULL</span>,</span>
<span> title <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">object</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> main <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">x</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span><spanclass="va">...</span></span>
<span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="co"># S3 method for rsi</span></span>
<span> title <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/deparse.html"class="external-link">deparse</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/substitute.html"class="external-link">substitute</a></span><spanclass="op">(</span><spanclass="va">object</span><spanclass="op">)</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span><spanclass="va">...</span></span>
<span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="co"># S3 method for rsi</span></span>
<dd><p>values created with <code><ahref="as.mic.html">as.mic()</a></code>, <code><ahref="as.disk.html">as.disk()</a></code> or <code><ahref="as.rsi.html">as.rsi()</a></code> (or their <code>random_*</code> variants, such as <code><ahref="random.html">random_mic()</a></code>)</p></dd>
<dt>mo</dt>
<dd><p>any (vector of) text that can be coerced to a valid microorganism code with <code><ahref="as.mo.html">as.mo()</a></code></p></dd>
<dd><p>interpretation guideline to use, defaults to the latest included EUCAST guideline, see <em>Details</em></p></dd>
<dt>main, title</dt>
<dd><p>title of the plot</p></dd>
<dt>xlab, ylab</dt>
<dd><p>axis title</p></dd>
<dt>colours_RSI</dt>
<dd><p>colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.</p></dd>
<dt>language</dt>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see <code><ahref="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <ahref="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>expand</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.</p></dd>
<p>The <code><ahref="https://ggplot2.tidyverse.org/reference/autoplot.html"class="external-link">autoplot()</a></code> functions return a <code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html"class="external-link">ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
<p>The <code><ahref="https://ggplot2.tidyverse.org/reference/fortify.html"class="external-link">fortify()</a></code> functions return a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> as an extension for usage in the <code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html"class="external-link">ggplot2::ggplot()</a></code> function.</p>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<spanclass="r-in"><span><spanclass="va">some_disk_values</span><spanclass="op"><-</span><spanclass="fu"><ahref="random.html">random_disk</a></span><spanclass="op">(</span>size <spanclass="op">=</span><spanclass="fl">100</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
<spanclass="r-in"><span><spanclass="fu">plot</span><spanclass="op">(</span><spanclass="va">some_mic_values</span>, mo <spanclass="op">=</span><spanclass="st">"S. aureus"</span>, ab <spanclass="op">=</span><spanclass="st">"ampicillin"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="fu">plot</span><spanclass="op">(</span><spanclass="va">some_disk_values</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="fu">plot</span><spanclass="op">(</span><spanclass="va">some_disk_values</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span>, language <spanclass="op">=</span><spanclass="st">"uk"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="fu"><ahref="https://ggplot2.tidyverse.org/reference/autoplot.html"class="external-link">autoplot</a></span><spanclass="op">(</span><spanclass="va">some_disk_values</span>, mo <spanclass="op">=</span><spanclass="st">"Escherichia coli"</span>, ab <spanclass="op">=</span><spanclass="st">"cipro"</span><spanclass="op">)</span></span></span>
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_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 <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
