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reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9015</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9016</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -437,8 +437,6 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 5 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_point()`).</span>
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
<span class="r-in"><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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
@ -448,8 +446,6 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Support in 27 languages"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 5 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_point()`).</span>
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
@ -460,16 +456,13 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"S. aureus"</span>, ab <span class="op">=</span> <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (any(cols_sub$cols == colours_SIR[2] &amp; cols_sub$count &gt; 0)) { legend_txt &lt;- c(legend_txt, "(SDD) Susceptible dose-dependent") legend_col &lt;- c(legend_col, colours_SIR[2])}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (any(cols_sub$cols == colours_SIR[3] &amp; cols_sub$count &gt; 0)) { legend_txt &lt;- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline))) legend_col &lt;- c(legend_col, colours_SIR[3])}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (any(cols_sub$cols == colours_SIR[3] &amp; cols_sub$count &gt; 0)) { legend_txt &lt;- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline))) legend_col &lt;- c(legend_col, colours_SIR[3])}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>