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(v1.0.1.9001) PCA unit tests
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Package: AMR
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Version: 1.0.1.9000
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Date: 2020-03-07
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Version: 1.0.1.9001
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Date: 2020-03-08
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -327,6 +327,7 @@ importFrom(stats,complete.cases)
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importFrom(stats,glm)
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importFrom(stats,lm)
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importFrom(stats,pchisq)
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importFrom(stats,prcomp)
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importFrom(stats,predict)
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importFrom(tidyr,pivot_longer)
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importFrom(tidyr,pivot_wider)
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2
NEWS.md
2
NEWS.md
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# AMR 1.0.1.9000
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# AMR 1.0.1.9001
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### New
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* Support for easy principal component analysis for AMR, using the new `pca()` function
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@ -33,6 +33,7 @@
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#' @param ellipse_prob statistical size of the ellipse in normal probability
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#' @param ellipse_size the size of the ellipse line
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#' @param ellipse_alpha the alpha (transparency) of the ellipse line
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#' @param points_size the size of the points
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#' @param points_alpha the alpha (transparency) of the points
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#' @param arrows a logical to indicate whether arrows should be drawn
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#' @param arrows_textsize the size of the text for variable names
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#' @param arrows_alpha the alpha (transparency) of the arrows and their text
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#' @param base_textsize the text size for all plot elements except the labels and arrows
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#' @param ... Parameters passed on to functions
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#' @source The [ggplot_pca()] function is based on the [ggbiplot()] function from the `ggbiplot` package by Vince Vu, as found on GitHub: <https://github.com/vqv/ggbiplot> (retrieved: 2 March 2020, their latest commit: [`7325e88`](https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9); 12 February 2015).
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#' @source The [ggplot_pca()] function is based on the `ggbiplot()` function from the `ggbiplot` package by Vince Vu, as found on GitHub: <https://github.com/vqv/ggbiplot> (retrieved: 2 March 2020, their latest commit: [`7325e88`](https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9); 12 February 2015).
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#'
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#' As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
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#' 1. Rewritten code to remove the dependency on packages `plyr`, `scales` and `grid`
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@ -324,10 +325,14 @@ pca_calculations <- function(pca_model,
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sigma <- var(cbind(x$xvar, x$yvar))
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mu <- c(mean(x$xvar), mean(x$yvar))
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ed <- sqrt(qchisq(ellipse_prob, df = 2))
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data.frame(sweep(circle %*% chol(sigma) * ed, 2, mu, FUN = "+"),
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el <- data.frame(sweep(circle %*% chol(sigma) * ed, 2, mu, FUN = "+"),
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groups = x$groups[1])
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names(el)[1:2] <- c("xvar", "yvar")
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el
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}))
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names(ell)[1:2] <- c("xvar", "yvar")
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if (NROW(ell) == 0) {
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ell <- NULL
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}
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} else {
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ell <- NULL
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}
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1
R/pca.R
1
R/pca.R
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#' The result of the [pca()] function is a [`prcomp`] object, with an additional attribute `non_numeric_cols` which is a vector with the column names of all columns that do not contain numeric values. These are probably the groups and labels, and will be used by [ggplot_pca()].
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#' @rdname pca
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#' @exportMethod prcomp.data.frame
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#' @importFrom stats prcomp
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#' @export
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#' @examples
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#' # `example_isolates` is a dataset available in the AMR package.
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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@ -226,9 +226,9 @@
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</div>
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<div id="amr-1019000" class="section level1">
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<div id="amr-1019001" class="section level1">
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<h1 class="page-header">
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<a href="#amr-1019000" class="anchor"></a>AMR 1.0.1.9000<small> Unreleased </small>
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<a href="#amr-1019001" class="anchor"></a>AMR 1.0.1.9001<small> Unreleased </small>
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</h1>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-1019000">1.0.1.9000</a></li>
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<li><a href="#amr-1019001">1.0.1.9001</a></li>
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<li><a href="#amr-101">1.0.1</a></li>
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<li><a href="#amr-100">1.0.0</a></li>
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<li><a href="#amr-090">0.9.0</a></li>
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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</li>
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<li>
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<a href="../articles/PCA.html">
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<span class="fa fa-compress-alt"></span>
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<span class="fa fa-compress"></span>
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Conduct Principal Component Analysis for AMR
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Conduct principal component analysis for AMR
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</a>
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</li>
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<li>
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<th>ellipse_alpha</th>
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<td><p>the alpha (transparency) of the ellipse line</p></td>
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</tr>
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<tr>
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<th>points_size</th>
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<td><p>the size of the points</p></td>
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</tr>
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<tr>
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<th>points_alpha</th>
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<td><p>the alpha (transparency) of the points</p></td>
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@ -78,7 +78,7 @@
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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">1.0.1.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
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</span>
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</div>
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\alias{ggplot_pca}
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\title{PCA biplot with \code{ggplot2}}
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\source{
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The \code{\link[=ggplot_pca]{ggplot_pca()}} function is based on the \code{\link[=ggbiplot]{ggbiplot()}} function from the \code{ggbiplot} package by Vince Vu, as found on GitHub: \url{https://github.com/vqv/ggbiplot} (retrieved: 2 March 2020, their latest commit: \href{https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9}{\code{7325e88}}; 12 February 2015).
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The \code{\link[=ggplot_pca]{ggplot_pca()}} function is based on the \code{ggbiplot()} function from the \code{ggbiplot} package by Vince Vu, as found on GitHub: \url{https://github.com/vqv/ggbiplot} (retrieved: 2 March 2020, their latest commit: \href{https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9}{\code{7325e88}}; 12 February 2015).
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As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
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\enumerate{
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@ -71,6 +71,8 @@ ggplot_pca(
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\item{ellipse_alpha}{the alpha (transparency) of the ellipse line}
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\item{points_size}{the size of the points}
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\item{points_alpha}{the alpha (transparency) of the points}
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\item{arrows}{a logical to indicate whether arrows should be drawn}
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37
tests/testthat/test-pca.R
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37
tests/testthat/test-pca.R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("pca.R")
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test_that("PCA works", {
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library(dplyr)
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resistance_data <- example_isolates %>%
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filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>%
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select(mo, AMC, CXM, CTX, TOB, TMP) %>%
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group_by(order = mo_order(mo), # group on anything, like order
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genus = mo_genus(mo)) %>% # and genus as we do here
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summarise_if(is.rsi, resistance, minimum = 0)
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expect_s3_class(pca(resistance_data), "prcomp")
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expect_s3_class(prcomp(resistance_data), "prcomp")
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ggplot_pca(pca(resistance_data), ellipse = TRUE)
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})
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