P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 21:01:57 +02:00
Code Releases Activity

(v1.3.0.9001) website update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
parent 0d9602a6a9
commit 7d16bec21f
79 changed files with 2221 additions and 1974 deletions
Download Patch File Download Diff File Expand all files Collapse all files

84
docs/reference/ggplot_pca.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>PCA biplot with <code>ggplot2</code> — ggplot_pca • AMR (for R)</title>
<title>PCA biplot with ggplot2 — ggplot_pca • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
<meta property="og:title" content="PCA biplot with ggplot2 — ggplot_pca" />
<meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -236,28 +236,28 @@
</div>
<pre class="usage"><span class='fu'>ggplot_pca</span>(
<span class='no'>x</span>,
<span class='kw'>choices</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>,
<span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>pc.biplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>labels_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>labels_text_placement</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
<span class='kw'>groups</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ellipse</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>ellipse_prob</span> <span class='kw'>=</span> <span class='fl'>0.68</span>,
<span class='kw'>ellipse_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>ellipse_alpha</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>points_size</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>points_alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>,
<span class='kw'>arrows</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>arrows_colour</span> <span class='kw'>=</span> <span class='st'>"darkblue"</span>,
<span class='kw'>arrows_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>arrows_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>arrows_textangled</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>arrows_alpha</span> <span class='kw'>=</span> <span class='fl'>0.75</span>,
<span class='kw'>base_textsize</span> <span class='kw'>=</span> <span class='fl'>10</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
choices = <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
scale = <span class='fl'>TRUE</span>,
pc.biplot = <span class='fl'>TRUE</span>,
labels = <span class='kw'>NULL</span>,
labels_textsize = <span class='fl'>3</span>,
labels_text_placement = <span class='fl'>1.5</span>,
groups = <span class='kw'>NULL</span>,
ellipse = <span class='fl'>TRUE</span>,
ellipse_prob = <span class='fl'>0.68</span>,
ellipse_size = <span class='fl'>0.5</span>,
ellipse_alpha = <span class='fl'>0.5</span>,
points_size = <span class='fl'>2</span>,
points_alpha = <span class='fl'>0.25</span>,
arrows = <span class='fl'>TRUE</span>,
arrows_colour = <span class='st'>"darkblue"</span>,
arrows_size = <span class='fl'>0.5</span>,
arrows_textsize = <span class='fl'>3</span>,
arrows_textangled = <span class='fl'>TRUE</span>,
arrows_alpha = <span class='fl'>0.75</span>,
base_textsize = <span class='fl'>10</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -388,24 +388,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># See ?example_isolates.</span>
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<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='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='kw'>pca_model</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<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'>%&gt;%</span>
<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'>%&gt;%</span>
<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'>%&gt;%</span>
<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>)
<span class='co'># old (base R)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_model</span>)
<span class='co'># new </span>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Title here"</span>)
<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>)
<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>)) {
<span class='fu'>ggplot_pca</span>(<span class='kw'>pca_model</span>) <span class='op'>+</span>
<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='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='st'>"Title here"</span>)
}
}</pre>
</div>
@ -423,7 +423,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>