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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
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parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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14
R/ggplot_pca.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -232,7 +236,7 @@ ggplot_pca <- function(x,
}
# Overlay a concentration ellipse if there are groups
if (!is.null(df.u$groups) & !is.null(ell) & isTRUE(ellipse)) {
if (!is.null(df.u$groups) && !is.null(ell) && isTRUE(ellipse)) {
g <- g + ggplot2::geom_path(
data = ell,
ggplot2::aes(colour = groups, group = groups),
@ -319,7 +323,7 @@ pca_calculations <- function(pca_model,
error = function(e) NULL
)
}
if (!is.null(groups) & is.null(labels)) {
if (!is.null(groups) && is.null(labels)) {
# turn them around
labels <- groups
groups <- NULL