mirror of
https://github.com/msberends/AMR.git
synced 2025-09-07 02:09:37 +02:00
(v1.1.0.9019) mo_source fix
This commit is contained in:
@@ -39,7 +39,7 @@
|
||||
</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">1.1.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9019</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -186,7 +186,7 @@
|
||||
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">15 April 2020</h4>
|
||||
<h4 class="date">25 May 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>PCA.Rmd</code></div>
|
||||
@@ -217,47 +217,47 @@
|
||||
<span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span>
|
||||
<span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
|
||||
<span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span>
|
||||
<span class="co"># $ mo <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…</span>
|
||||
<span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
|
||||
<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
|
||||
<span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
|
||||
<span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
|
||||
<span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
|
||||
<span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
|
||||
<span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
|
||||
<span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
|
||||
<span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></body></html></div>
|
||||
<span class="co"># $ mo <mo> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STP…</span>
|
||||
<span class="co"># $ PEN <ord> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ OXA <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FLC <ord> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ AMX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ AMC <ord> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
|
||||
<span class="co"># $ AMP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TZP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CZO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FEP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CXM <ord> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
|
||||
<span class="co"># $ FOX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CTX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ CAZ <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
|
||||
<span class="co"># $ CRO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ GEN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TOB <ord> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
|
||||
<span class="co"># $ AMK <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ KAN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TMP <ord> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
|
||||
<span class="co"># $ SXT <ord> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
|
||||
<span class="co"># $ NIT <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FOS <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ LNZ <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ CIP <ord> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ MFX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ VAN <ord> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ TEC <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ TCY <ord> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
|
||||
<span class="co"># $ TGC <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ DOX <ord> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
|
||||
<span class="co"># $ ERY <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ CLI <ord> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ AZM <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ IPM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ MEM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ MTR <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CHL <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ COL <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ MUP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ RIF <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></body></html></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">resistance_data</span> <span class="kw"><-</span> <span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">order</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">mo</span>), <span class="co"># group on anything, like order</span>
|
||||
@@ -283,7 +283,7 @@
|
||||
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">pca_result</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span>(<span class="no">resistance_data</span>)
|
||||
<span class="co"># NOTE: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.</span>
|
||||
<span class="co"># NOTE: Columns selected for PCA: AMC CXM CTX CAZ GEN TOB TMP SXT.</span>
|
||||
<span class="co"># Total observations available: 7.</span></pre></body></html></div>
|
||||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">pca_result</span>)
|
||||
@@ -303,8 +303,7 @@
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
|
||||
<p>You can also print an ellipse per group, and edit the appearance:</p>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r">
|
||||
<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>, <span class="kw">ellipse</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>, <span class="kw">ellipse</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +
|
||||
<span class="kw pkg">ggplot2</span><span class="kw ns">::</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">"An AMR/PCA biplot!"</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
|
||||
</div>
|
||||
@@ -325,7 +324,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user