mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
76 lines
3.4 KiB
R
76 lines
3.4 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# 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 and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# 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 the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
resistance_data <- structure(list(
|
|
order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
|
|
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
|
|
AMC = c(0.00425, 0.13062, 0.10344),
|
|
CXM = c(0.00425, 0.05376, 0.10344),
|
|
CTX = c(0.00000, 0.02396, 0.05172),
|
|
TOB = c(0.02325, 0.02597, 0.10344),
|
|
TMP = c(0.08387, 0.39141, 0.18367)
|
|
),
|
|
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
|
|
row.names = c(NA, -3L),
|
|
groups = structure(list(
|
|
order = c("Bacillales", "Enterobacterales"),
|
|
.rows = list(1L, 2:3)
|
|
),
|
|
row.names = c(NA, -2L),
|
|
class = c("tbl_df", "tbl", "data.frame"),
|
|
.drop = TRUE
|
|
)
|
|
)
|
|
pca_model <- pca(resistance_data)
|
|
expect_inherits(pca_model, "pca")
|
|
|
|
pdf(NULL) # prevent Rplots.pdf being created
|
|
|
|
if (AMR:::pkg_is_available("ggplot2")) {
|
|
ggplot_pca(pca_model, ellipse = TRUE)
|
|
ggplot_pca(pca_model, arrows_textangled = FALSE)
|
|
}
|
|
|
|
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
|
resistance_data <- example_isolates %>%
|
|
group_by(
|
|
order = mo_order(mo),
|
|
genus = mo_genus(mo)
|
|
) %>%
|
|
summarise_if(is.sir, resistance, minimum = 0)
|
|
pca_result <- resistance_data %>%
|
|
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
|
|
expect_inherits(pca_result, "prcomp")
|
|
|
|
if (AMR:::pkg_is_available("ggplot2")) {
|
|
ggplot_pca(pca_result, ellipse = TRUE)
|
|
ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
|
|
}
|
|
}
|