mirror of https://github.com/msberends/AMR.git
(v1.0.1.9001) PCA unit tests
This commit is contained in:
parent
fa0d9c58d9
commit
9fc858f208
|
|
@ -1,6 +1,6 @@
|
|||
Package: AMR
|
||||
Version: 1.0.1.9000
|
||||
Date: 2020-03-07
|
||||
Version: 1.0.1.9001
|
||||
Date: 2020-03-08
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
|
|
|
|||
|
|
@ -327,6 +327,7 @@ importFrom(stats,complete.cases)
|
|||
importFrom(stats,glm)
|
||||
importFrom(stats,lm)
|
||||
importFrom(stats,pchisq)
|
||||
importFrom(stats,prcomp)
|
||||
importFrom(stats,predict)
|
||||
importFrom(tidyr,pivot_longer)
|
||||
importFrom(tidyr,pivot_wider)
|
||||
|
|
|
|||
2
NEWS.md
2
NEWS.md
|
|
@ -1,4 +1,4 @@
|
|||
# AMR 1.0.1.9000
|
||||
# AMR 1.0.1.9001
|
||||
|
||||
### New
|
||||
* Support for easy principal component analysis for AMR, using the new `pca()` function
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@
|
|||
#' @param ellipse_prob statistical size of the ellipse in normal probability
|
||||
#' @param ellipse_size the size of the ellipse line
|
||||
#' @param ellipse_alpha the alpha (transparency) of the ellipse line
|
||||
#' @param points_size the size of the points
|
||||
#' @param points_alpha the alpha (transparency) of the points
|
||||
#' @param arrows a logical to indicate whether arrows should be drawn
|
||||
#' @param arrows_textsize the size of the text for variable names
|
||||
|
|
@ -42,7 +43,7 @@
|
|||
#' @param arrows_alpha the alpha (transparency) of the arrows and their text
|
||||
#' @param base_textsize the text size for all plot elements except the labels and arrows
|
||||
#' @param ... Parameters passed on to functions
|
||||
#' @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).
|
||||
#' @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).
|
||||
#'
|
||||
#' As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
|
||||
#' 1. Rewritten code to remove the dependency on packages `plyr`, `scales` and `grid`
|
||||
|
|
@ -324,14 +325,18 @@ pca_calculations <- function(pca_model,
|
|||
sigma <- var(cbind(x$xvar, x$yvar))
|
||||
mu <- c(mean(x$xvar), mean(x$yvar))
|
||||
ed <- sqrt(qchisq(ellipse_prob, df = 2))
|
||||
data.frame(sweep(circle %*% chol(sigma) * ed, 2, mu, FUN = "+"),
|
||||
el <- data.frame(sweep(circle %*% chol(sigma) * ed, 2, mu, FUN = "+"),
|
||||
groups = x$groups[1])
|
||||
names(el)[1:2] <- c("xvar", "yvar")
|
||||
el
|
||||
}))
|
||||
names(ell)[1:2] <- c("xvar", "yvar")
|
||||
if (NROW(ell) == 0) {
|
||||
ell <- NULL
|
||||
}
|
||||
} else {
|
||||
ell <- NULL
|
||||
}
|
||||
|
||||
|
||||
list(nobs.factor = nobs.factor,
|
||||
d = d,
|
||||
u = u,
|
||||
|
|
|
|||
1
R/pca.R
1
R/pca.R
|
|
@ -31,6 +31,7 @@
|
|||
#' 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()].
|
||||
#' @rdname pca
|
||||
#' @exportMethod prcomp.data.frame
|
||||
#' @importFrom stats prcomp
|
||||
#' @export
|
||||
#' @examples
|
||||
#' # `example_isolates` is a dataset available in the AMR package.
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -226,9 +226,9 @@
|
|||
|
||||
</div>
|
||||
|
||||
<div id="amr-1019000" class="section level1">
|
||||
<div id="amr-1019001" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-1019000" class="anchor"></a>AMR 1.0.1.9000<small> Unreleased </small>
|
||||
<a href="#amr-1019001" class="anchor"></a>AMR 1.0.1.9001<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
|
@ -1489,7 +1489,7 @@
|
|||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-1019000">1.0.1.9000</a></li>
|
||||
<li><a href="#amr-1019001">1.0.1.9001</a></li>
|
||||
<li><a href="#amr-101">1.0.1</a></li>
|
||||
<li><a href="#amr-100">1.0.0</a></li>
|
||||
<li><a href="#amr-090">0.9.0</a></li>
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -117,9 +117,9 @@
|
|||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress-alt"></span>
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct Principal Component Analysis for AMR
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
|
|
@ -307,6 +307,10 @@
|
|||
<th>ellipse_alpha</th>
|
||||
<td><p>the alpha (transparency) of the ellipse line</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>points_size</th>
|
||||
<td><p>the size of the points</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>points_alpha</th>
|
||||
<td><p>the alpha (transparency) of the points</p></td>
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</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">1.0.1.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
\alias{ggplot_pca}
|
||||
\title{PCA biplot with \code{ggplot2}}
|
||||
\source{
|
||||
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).
|
||||
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).
|
||||
|
||||
As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
|
||||
\enumerate{
|
||||
|
|
@ -71,6 +71,8 @@ ggplot_pca(
|
|||
|
||||
\item{ellipse_alpha}{the alpha (transparency) of the ellipse line}
|
||||
|
||||
\item{points_size}{the size of the points}
|
||||
|
||||
\item{points_alpha}{the alpha (transparency) of the points}
|
||||
|
||||
\item{arrows}{a logical to indicate whether arrows should be drawn}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,37 @@
|
|||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://gitlab.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("pca.R")
|
||||
|
||||
test_that("PCA works", {
|
||||
library(dplyr)
|
||||
resistance_data <- example_isolates %>%
|
||||
filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>%
|
||||
select(mo, AMC, CXM, CTX, TOB, TMP) %>%
|
||||
group_by(order = mo_order(mo), # group on anything, like order
|
||||
genus = mo_genus(mo)) %>% # and genus as we do here
|
||||
summarise_if(is.rsi, resistance, minimum = 0)
|
||||
|
||||
expect_s3_class(pca(resistance_data), "prcomp")
|
||||
expect_s3_class(prcomp(resistance_data), "prcomp")
|
||||
|
||||
ggplot_pca(pca(resistance_data), ellipse = TRUE)
|
||||
})
|
||||
Loading…
Reference in New Issue