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Especially the scale_*_mic() functions are relevant wrappers to plot MIC values for ggplot2. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values."><title>Plotting for Classes sir, 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-5.3.1/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><linkhref="../deps/Lato-0.4.9/font.css"rel="stylesheet"><linkhref="../deps/Fira_Code-0.4.9/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/2.0.11/clipboard.min.js"integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw=="crossorigin="anonymous"referrerpolicy="no-referrer"></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 sir, mic and disk — plot"><metaproperty="og:description"content="Functionstoplotclassessir,micanddisk,withsupportforbaseRandggplot2.
Especially the scale_*_mic() functions are relevant wrappers to plot MIC values for ggplot2. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values."><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><scriptsrc="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]>
<p>Functions to plot classes <code>sir</code>, <code>mic</code> and <code>disk</code>, with support for base <spanstyle="R">R</span> and <code>ggplot2</code>.</p>
<p>Especially the <code>scale_*_mic()</code> functions are relevant wrappers to plot MIC values for <code>ggplot2</code>. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.</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> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Frequency"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <spanclass="op">=</span><spanclass="va">language</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> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Frequency"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <spanclass="op">=</span><spanclass="va">language</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> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Frequency"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Disk diffusion diameter (mm)"</span>, language <spanclass="op">=</span><spanclass="va">language</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> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Frequency"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Disk diffusion diameter (mm)"</span>, language <spanclass="op">=</span><spanclass="va">language</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> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Percentage"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Antimicrobial Interpretation"</span>, language <spanclass="op">=</span><spanclass="va">language</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> 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> xlab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Antimicrobial Interpretation"</span>, language <spanclass="op">=</span><spanclass="va">language</span><spanclass="op">)</span>,</span>
<span> ylab <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">translate_AMR</a></span><spanclass="op">(</span><spanclass="st">"Frequency"</span>, language <spanclass="op">=</span><spanclass="va">language</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>
<dd><p>a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> specifying how to handle operators (such as <code>></code> and <code><=</code>) in the input. Accepts one of three values: <code>"all"</code> (or <code>TRUE</code>) to keep all operators, <code>"none"</code> (or <code>FALSE</code>) to remove all operators, or <code>"edges"</code> to keep operators only at both ends of the range.</p></dd>
<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to remove intermediate MIC values, defaults to <code>FALSE</code></p></dd>
<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.sir.html">as.sir()</a></code> (or their <code>random_*</code> variants, such as <code><ahref="random.html">random_mic()</a></code>)</p></dd>
<dd><p>colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.</p></dd>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see <code><ahref="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the <ahref="AMR-options.html">package option</a><code><ahref="AMR-options.html">AMR_locale</a></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>
<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>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <ahref="AMR-options.html">package option</a><code><ahref="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <ahref="AMR-options.html">package option</a><code><ahref="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</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">"nl"</span><spanclass="op">)</span></span></span>
<spanclass="r-in"><span><spanclass="fu"><ahref="https://ggplot2.tidyverse.org/reference/labs.html"class="external-link">labs</a></span><spanclass="op">(</span>title <spanclass="op">=</span><spanclass="st">"with scale_x_mic() using a manual range"</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><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>
