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<h1>AMR Plots with <code>ggplot2</code></h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ggplot_rsi.R" class="external-link"><code>R/ggplot_rsi.R</code></a></small>
<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" class="external-link">ggplot2</a> functions.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><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" class="external-link">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_AMR_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" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>, R <span class="op">=</span>
<span class="st">"#ED553B"</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>,
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" class="external-link">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_AMR_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" class="external-link">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" class="external-link">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><span class="va">...</span>, aesthetics <span class="op">=</span> <span class="st">"fill"</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_AMR_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>,
datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>data</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">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></dd>
<dt>position</dt>
<dd><p>position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></dd>
<dt>x</dt>
<dd><p>variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></dd>
<dt>fill</dt>
<dd><p>variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></dd>
<dt>facet</dt>
<dd><p>variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></dd>
<dt>breaks</dt>
<dd><p>a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions</p></dd>
<dt>limits</dt>
<dd><p>a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></dd>
<dt>translate_ab</dt>
<dd><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></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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></dd>
<dt>combine_IR</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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></dd>
<dt>minimum</dt>
<dd><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></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>nrow</dt>
<dd><p>(when using <code>facet</code>) number of rows</p></dd>
<dt>colours</dt>
<dd><p>a named vactor with colour to be used for filling. The default colours are colour-blind friendly.</p></dd>
<dt>datalabels</dt>
<dd><p>show datalabels using <code>labels_rsi_count()</code></p></dd>
<dt>datalabels.size</dt>
<dd><p>size of the datalabels</p></dd>
<dt>datalabels.colour</dt>
<dd><p>colour of the datalabels</p></dd>
<dt>title</dt>
<dd><p>text to show as title of the plot</p></dd>
<dt>subtitle</dt>
<dd><p>text to show as subtitle of the plot</p></dd>
<dt>caption</dt>
<dd><p>text to show as caption of the plot</p></dd>
<dt>x.title</dt>
<dd><p>text to show as x axis description</p></dd>
<dt>y.title</dt>
<dd><p>text to show as y axis description</p></dd>
<dt>...</dt>
<dd><p>other arguments passed on to <code>geom_rsi()</code> or, in case of <code>scale_rsi_colours()</code>, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See <em>Examples</em>.</p></dd>
<dt>aesthetics</dt>
<dd><p>aesthetics to apply the colours to, defaults to "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></dd>
</dl></div>
<div id="details">
<h2>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><div class="section">
<h3 id="the-functions">The Functions<a class="anchor" aria-label="anchor" href="#the-functions"></a></h3>
<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" class="external-link">ggplot2::facet_wrap()</a></code>.</p>
<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" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p>
<p><code>theme_rsi()</code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p>
<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" class="external-link">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>
</div>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
<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>.</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="co"># get antimicrobial results for drugs against a UTI:</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></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">%&gt;%</a></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">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>
<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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">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" class="external-link">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>
<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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu">ggplot_rsi</span><span class="op">(</span><span class="op">)</span>
<span class="co"># get only proportions and no counts:</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span class="co"># add other ggplot2 arguments as you like:</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span class="co"># you can alter the colours with colour names:</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">AMX</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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" class="external-link">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>
<span class="co"># but you can also use the built-in colour-blind friendly colours for</span>
<span class="co"># your plots, where "S" is green, "I" is yellow and "R" is red:</span>
<span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value1"</span>, <span class="st">"Value2"</span>, <span class="st">"Value3"</span><span class="op">)</span>,
y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>,
z <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value4"</span>, <span class="st">"Value5"</span>, <span class="st">"Value6"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">x</span>, y <span class="op">=</span> <span class="va">y</span>, fill <span class="op">=</span> <span class="va">z</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>
<span class="fu">scale_rsi_colours</span><span class="op">(</span>Value4 <span class="op">=</span> <span class="st">"S"</span>, Value5 <span class="op">=</span> <span class="st">"I"</span>, Value6 <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
<span class="co"># resistance of ciprofloxacine per age group</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">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="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<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" class="external-link">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<span class="co"># a shorter version which also adjusts data label colours:</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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>
<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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="co"># select only UTI-specific 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">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"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</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><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></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="op">}</span>
<span class="co"># }</span>
</code></pre></div>
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