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(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening
This commit is contained in:
@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9001</span>
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</span>
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</div>
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@ -242,30 +242,30 @@
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<p>Produces a <code>ggplot2</code> variant of a so-called <a href='https://en.wikipedia.org/wiki/Biplot'>biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href='https://rdrr.io/r/stats/biplot.html'>biplot()</a></code> function.</p>
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</div>
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<pre class="usage"><span class='fu'>ggplot_pca</span>(
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<span class='kw'>x</span>,
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choices = <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
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scale = <span class='fl'>TRUE</span>,
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pc.biplot = <span class='fl'>TRUE</span>,
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labels = <span class='kw'>NULL</span>,
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labels_textsize = <span class='fl'>3</span>,
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labels_text_placement = <span class='fl'>1.5</span>,
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groups = <span class='kw'>NULL</span>,
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ellipse = <span class='fl'>TRUE</span>,
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ellipse_prob = <span class='fl'>0.68</span>,
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ellipse_size = <span class='fl'>0.5</span>,
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ellipse_alpha = <span class='fl'>0.5</span>,
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points_size = <span class='fl'>2</span>,
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points_alpha = <span class='fl'>0.25</span>,
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arrows = <span class='fl'>TRUE</span>,
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arrows_colour = <span class='st'>"darkblue"</span>,
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arrows_size = <span class='fl'>0.5</span>,
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arrows_textsize = <span class='fl'>3</span>,
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arrows_textangled = <span class='fl'>TRUE</span>,
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arrows_alpha = <span class='fl'>0.75</span>,
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base_textsize = <span class='fl'>10</span>,
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<span class='kw'>...</span>
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)</pre>
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<pre class="usage"><span class='fu'>ggplot_pca</span><span class='op'>(</span>
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<span class='va'>x</span>,
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choices <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
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scale <span class='op'>=</span> <span class='fl'>1</span>,
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pc.biplot <span class='op'>=</span> <span class='cn'>TRUE</span>,
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labels <span class='op'>=</span> <span class='cn'>NULL</span>,
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labels_textsize <span class='op'>=</span> <span class='fl'>3</span>,
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labels_text_placement <span class='op'>=</span> <span class='fl'>1.5</span>,
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groups <span class='op'>=</span> <span class='cn'>NULL</span>,
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ellipse <span class='op'>=</span> <span class='cn'>TRUE</span>,
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ellipse_prob <span class='op'>=</span> <span class='fl'>0.68</span>,
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ellipse_size <span class='op'>=</span> <span class='fl'>0.5</span>,
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ellipse_alpha <span class='op'>=</span> <span class='fl'>0.5</span>,
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points_size <span class='op'>=</span> <span class='fl'>2</span>,
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points_alpha <span class='op'>=</span> <span class='fl'>0.25</span>,
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arrows <span class='op'>=</span> <span class='cn'>TRUE</span>,
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arrows_colour <span class='op'>=</span> <span class='st'>"darkblue"</span>,
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arrows_size <span class='op'>=</span> <span class='fl'>0.5</span>,
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arrows_textsize <span class='op'>=</span> <span class='fl'>3</span>,
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arrows_textangled <span class='op'>=</span> <span class='cn'>TRUE</span>,
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arrows_alpha <span class='op'>=</span> <span class='fl'>0.75</span>,
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base_textsize <span class='op'>=</span> <span class='fl'>10</span>,
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<span class='va'>...</span>
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<span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -375,8 +375,9 @@
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<p>As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:</p><ol>
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<li><p>Rewritten code to remove the dependency on packages <code>plyr</code>, <code>scales</code> and <code>grid</code></p></li>
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<li><p>Parametrised more options, like arrow and ellipse settings</p></li>
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<li><p>Hardened all input possibilities by defining the exact type of user input for every parameter</p></li>
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<li><p>Added total amount of explained variance as a caption in the plot</p></li>
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<li><p>Cleaned all syntax based on the <code>lintr</code> package and added integrity checks</p></li>
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<li><p>Cleaned all syntax based on the <code>lintr</code> package, fixed grammatical errors and added integrity checks</p></li>
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<li><p>Updated documentation</p></li>
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</ol>
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@ -395,25 +396,25 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<span class='co'># See ?example_isolates.</span>
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<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
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<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
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<span class='kw'>pca_model</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>) <span class='op'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(species = <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='kw'>mo</span>)) <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='kw'>is.rsi</span>, <span class='kw'>resistance</span>) <span class='op'>%>%</span>
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<span class='fu'><a href='pca.html'>pca</a></span>(<span class='kw'>FLC</span>, <span class='kw'>AMC</span>, <span class='kw'>CXM</span>, <span class='kw'>GEN</span>, <span class='kw'>TOB</span>, <span class='kw'>TMP</span>, <span class='kw'>SXT</span>, <span class='kw'>CIP</span>, <span class='kw'>TEC</span>, <span class='kw'>TCY</span>, <span class='kw'>ERY</span>)
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<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='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
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<span class='va'>pca_model</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"Staphylococcus"</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>species <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> <span class='op'>(</span><span class='va'>is.rsi</span>, <span class='va'>resistance</span><span class='op'>)</span> <span class='op'>%>%</span>
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<span class='fu'><a href='pca.html'>pca</a></span><span class='op'>(</span><span class='va'>FLC</span>, <span class='va'>AMC</span>, <span class='va'>CXM</span>, <span class='va'>GEN</span>, <span class='va'>TOB</span>, <span class='va'>TMP</span>, <span class='va'>SXT</span>, <span class='va'>CIP</span>, <span class='va'>TEC</span>, <span class='va'>TCY</span>, <span class='va'>ERY</span><span class='op'>)</span>
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<span class='co'># old (base R)</span>
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_model</span>)
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span><span class='op'>(</span><span class='va'>pca_model</span><span class='op'>)</span>
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<span class='co'># new </span>
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<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>)
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<span class='fu'>ggplot_pca</span><span class='op'>(</span><span class='va'>pca_model</span><span class='op'>)</span>
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<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
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<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>) <span class='op'>+</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() <span class='op'>+</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='st'>"Title here"</span>)
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}
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}
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<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'>)</span> <span class='op'>{</span>
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<span class='fu'>ggplot_pca</span><span class='op'>(</span><span class='va'>pca_model</span><span class='op'>)</span> <span class='op'>+</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>"Title here"</span><span class='op'>)</span>
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<span class='op'>}</span>
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<span class='op'>}</span>
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</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@ -430,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</div>
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</footer>
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