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Conduct Principal Component Analysis for AMR
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<img src="../logo.svg" class="logo" alt=""><h1>Principal Component Analysis (for AMR)</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/pca.R" class="external-link"><code>R/pca.R</code></a></small>
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<div class="d-none name"><code>pca.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pca</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> <span class="va">...</span>,</span>
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<span> retx <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> center <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> scale. <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> tol <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> rank. <span class="op">=</span> <span class="cn">NULL</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> columns</p></dd>
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<dt>...</dt>
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<dd><p>columns of <code>x</code> to be selected for PCA, can be unquoted since it supports quasiquotation.</p></dd>
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<dt>retx</dt>
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<dd><p>a logical value indicating whether the rotated variables
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should be returned.</p></dd>
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<dt>center</dt>
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<dd><p>a logical value indicating whether the variables
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should be shifted to be zero centered. Alternately, a vector of
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length equal the number of columns of <code>x</code> can be supplied.
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The value is passed to <code>scale</code>.</p></dd>
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<dt>scale.</dt>
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<dd><p>a logical value indicating whether the variables should
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be scaled to have unit variance before the analysis takes
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place. The default is <code>FALSE</code> for consistency with S, but
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in general scaling is advisable. Alternatively, a vector of length
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equal the number of columns of <code>x</code> can be supplied. The
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value is passed to <code><a href="https://rdrr.io/r/base/scale.html" class="external-link">scale</a></code>.</p></dd>
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<dt>tol</dt>
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<dd><p>a value indicating the magnitude below which components
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should be omitted. (Components are omitted if their
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standard deviations are less than or equal to <code>tol</code> times the
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standard deviation of the first component.) With the default null
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setting, no components are omitted (unless <code>rank.</code> is specified
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less than <code>min(dim(x))</code>.). Other settings for tol could be
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<code>tol = 0</code> or <code>tol = sqrt(.Machine$double.eps)</code>, which
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would omit essentially constant components.</p></dd>
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<dt>rank.</dt>
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<dd><p>optionally, a number specifying the maximal rank, i.e.,
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maximal number of principal components to be used. Can be set as
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alternative or in addition to <code>tol</code>, useful notably when the
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desired rank is considerably smaller than the dimensions of the matrix.</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>An object of classes pca and <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp</a></p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>The <code>pca()</code> function takes a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> as input and performs the actual PCA with the <span style="R">R</span> function <code><a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp()</a></code>.</p>
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<p>The result of the <code>pca()</code> function is a <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp</a> object, with an additional attribute <code>non_numeric_cols</code> which is a vector with the column names of all columns that do not contain <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values. These are probably the groups and labels, and will be used by <code><a href="ggplot_pca.html">ggplot_pca()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
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<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="co"># calculate the resistance per group first</span></span></span>
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<span class="r-in"><span> <span class="va">resistance_data</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">%>%</a></span></span></span>
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<span class="r-in"><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></span>
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<span class="r-in"><span> order <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span></span>
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<span class="r-in"><span> genus <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></span>
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<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
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<span class="r-in"><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="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.sir</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># now conduct PCA for certain antimicrobial drugs</span></span></span>
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<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu">pca</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="va">pca_result</span></span></span>
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||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># old base R plotting method:</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># new ggplot2 plotting method using this package:</span></span></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="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Title here"</span><span class="op">)</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">#></span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> The first warning was:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> only_all_tested = FALSE) ...`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` and `genus = "Enterococcus"`.</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
|
||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> "TMP", and "TOB". Total observations available: 7.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> Groups (n=4, named as 'order'):</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-plt img"><img src="pca-1.png" alt="" width="700" height="433"></span>
|
||
<span class="r-plt img"><img src="pca-2.png" alt="" width="700" height="433"></span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_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 <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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</div>
|
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<div class="pkgdown-footer-right">
|
||
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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