mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:46:11 +01:00
455 lines
20 KiB
R
Executable File
455 lines
20 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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 analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' AMR plots with `ggplot2`
|
|
#'
|
|
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
|
|
#' @inheritSection lifecycle Maturing lifecycle
|
|
#' @param data a [data.frame] with column(s) of class [`rsi`] (see [as.rsi()])
|
|
#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
|
|
#' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
|
|
#' @param fill variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
|
|
#' @param breaks numeric vector of positions
|
|
#' @param limits numeric vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
|
|
#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
|
|
#' @inheritParams proportion
|
|
#' @param nrow (when using `facet`) number of rows
|
|
#' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be `FALSE` to use default [ggplot2][[ggplot2::ggplot()] colours.
|
|
#' @param datalabels show datalabels using [labels_rsi_count()]
|
|
#' @param datalabels.size size of the datalabels
|
|
#' @param datalabels.colour colour of the datalabels
|
|
#' @param title text to show as title of the plot
|
|
#' @param subtitle text to show as subtitle of the plot
|
|
#' @param caption text to show as caption of the plot
|
|
#' @param x.title text to show as x axis description
|
|
#' @param y.title text to show as y axis description
|
|
#' @param ... other parameters passed on to [geom_rsi()]
|
|
#' @details At default, the names of antibiotics will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` parameter. See [count_df()].
|
|
#'
|
|
#' ## The functions
|
|
#' [geom_rsi()] will take any variable from the data that has an [`rsi`] class (created with [as.rsi()]) using [rsi_df()] and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
|
|
#'
|
|
#' [facet_rsi()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
|
|
#'
|
|
#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
|
|
#'
|
|
#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_fill_manual()].
|
|
#'
|
|
#' [theme_rsi()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
|
|
#'
|
|
#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
|
|
#'
|
|
#' [ggplot_rsi()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See Examples.
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @examples
|
|
#' if (require("ggplot2") & require("dplyr")) {
|
|
#'
|
|
#' # get antimicrobial results for drugs against a UTI:
|
|
#' ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +
|
|
#' geom_rsi()
|
|
#'
|
|
#' # prettify the plot using some additional functions:
|
|
#' df <- example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)
|
|
#' ggplot(df) +
|
|
#' geom_rsi() +
|
|
#' scale_y_percent() +
|
|
#' scale_rsi_colours() +
|
|
#' labels_rsi_count() +
|
|
#' theme_rsi()
|
|
#'
|
|
#' # or better yet, simplify this using the wrapper function - a single command:
|
|
#' example_isolates %>%
|
|
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' ggplot_rsi()
|
|
#'
|
|
#' # get only proportions and no counts:
|
|
#' example_isolates %>%
|
|
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' ggplot_rsi(datalabels = FALSE)
|
|
#'
|
|
#' # add other ggplot2 parameters as you like:
|
|
#' example_isolates %>%
|
|
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' ggplot_rsi(width = 0.5,
|
|
#' colour = "black",
|
|
#' size = 1,
|
|
#' linetype = 2,
|
|
#' alpha = 0.25)
|
|
#'
|
|
#' example_isolates %>%
|
|
#' select(AMX) %>%
|
|
#' ggplot_rsi(colours = c(SI = "yellow"))
|
|
#'
|
|
#' }
|
|
#'
|
|
#' \donttest{
|
|
#'
|
|
#' # resistance of ciprofloxacine per age group
|
|
#' example_isolates %>%
|
|
#' mutate(first_isolate = first_isolate(.)) %>%
|
|
#' filter(first_isolate == TRUE,
|
|
#' mo == as.mo("E. coli")) %>%
|
|
#' # `age_groups` is also a function of this AMR package:
|
|
#' group_by(age_group = age_groups(age)) %>%
|
|
#' select(age_group,
|
|
#' CIP) %>%
|
|
#' ggplot_rsi(x = "age_group")
|
|
#'
|
|
#' # for colourblind mode, use divergent colours from the viridis package:
|
|
#' example_isolates %>%
|
|
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' ggplot_rsi() +
|
|
#' scale_fill_viridis_d()
|
|
#' # a shorter version which also adjusts data label colours:
|
|
#' example_isolates %>%
|
|
#' select(AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' ggplot_rsi(colours = FALSE)
|
|
#'
|
|
#'
|
|
#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
|
|
#' example_isolates %>%
|
|
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
|
|
#' group_by(hospital_id) %>%
|
|
#' ggplot_rsi(x = "hospital_id",
|
|
#' facet = "antibiotic",
|
|
#' nrow = 1,
|
|
#' title = "AMR of Anti-UTI Drugs Per Hospital",
|
|
#' x.title = "Hospital",
|
|
#' datalabels = FALSE)
|
|
#' }
|
|
ggplot_rsi <- function(data,
|
|
position = NULL,
|
|
x = "antibiotic",
|
|
fill = "interpretation",
|
|
# params = list(),
|
|
facet = NULL,
|
|
breaks = seq(0, 1, 0.1),
|
|
limits = NULL,
|
|
translate_ab = "name",
|
|
combine_SI = TRUE,
|
|
combine_IR = FALSE,
|
|
minimum = 30,
|
|
language = get_locale(),
|
|
nrow = NULL,
|
|
colours = c(S = "#61a8ff",
|
|
SI = "#61a8ff",
|
|
I = "#61f7ff",
|
|
IR = "#ff6961",
|
|
R = "#ff6961"),
|
|
datalabels = TRUE,
|
|
datalabels.size = 2.5,
|
|
datalabels.colour = "grey15",
|
|
title = NULL,
|
|
subtitle = NULL,
|
|
caption = NULL,
|
|
x.title = "Antimicrobial",
|
|
y.title = "Proportion",
|
|
...) {
|
|
|
|
stop_ifnot_installed("ggplot2")
|
|
meet_criteria(data, allow_class = "data.frame", contains_column_class = "rsi")
|
|
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
|
|
meet_criteria(x, allow_class = "character", has_length = 1)
|
|
meet_criteria(fill, allow_class = "character", has_length = 1)
|
|
meet_criteria(facet, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(breaks, allow_class = c("numeric", "integer"))
|
|
meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
|
|
meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
|
|
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
|
|
meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
|
|
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1)
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(colours, allow_class = c("character", "logical"))
|
|
meet_criteria(datalabels, allow_class = "logical", has_length = 1)
|
|
meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1)
|
|
meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
|
|
meet_criteria(title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(subtitle, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(caption, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(x.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
meet_criteria(y.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
|
|
# we work with aes_string later on
|
|
x_deparse <- deparse(substitute(x))
|
|
if (x_deparse != "x") {
|
|
x <- x_deparse
|
|
}
|
|
if (x %like% '".*"') {
|
|
x <- substr(x, 2, nchar(x) - 1)
|
|
}
|
|
facet_deparse <- deparse(substitute(facet))
|
|
if (facet_deparse != "facet") {
|
|
facet <- facet_deparse
|
|
}
|
|
if (facet %like% '".*"') {
|
|
facet <- substr(facet, 2, nchar(facet) - 1)
|
|
}
|
|
if (facet %in% c("NULL", "")) {
|
|
facet <- NULL
|
|
}
|
|
|
|
if (is.null(position)) {
|
|
position <- "fill"
|
|
}
|
|
|
|
p <- ggplot2::ggplot(data = data) +
|
|
geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab,
|
|
minimum = minimum, language = language,
|
|
combine_SI = combine_SI, combine_IR = combine_IR, ...) +
|
|
theme_rsi()
|
|
|
|
if (fill == "interpretation") {
|
|
# set RSI colours
|
|
if (isFALSE(colours) & missing(datalabels.colour)) {
|
|
# set datalabel colour to middle grey
|
|
datalabels.colour <- "grey50"
|
|
}
|
|
p <- p + scale_rsi_colours(colours = colours)
|
|
}
|
|
|
|
if (identical(position, "fill")) {
|
|
# proportions, so use y scale with percentage
|
|
p <- p + scale_y_percent(breaks = breaks, limits = limits)
|
|
}
|
|
|
|
if (datalabels == TRUE) {
|
|
p <- p + labels_rsi_count(position = position,
|
|
x = x,
|
|
translate_ab = translate_ab,
|
|
minimum = minimum,
|
|
language = language,
|
|
combine_SI = combine_SI,
|
|
combine_IR = combine_IR,
|
|
datalabels.size = datalabels.size,
|
|
datalabels.colour = datalabels.colour)
|
|
}
|
|
|
|
if (!is.null(facet)) {
|
|
p <- p + facet_rsi(facet = facet, nrow = nrow)
|
|
}
|
|
|
|
p <- p + ggplot2::labs(title = title,
|
|
subtitle = subtitle,
|
|
caption = caption,
|
|
x = x.title,
|
|
y = y.title)
|
|
|
|
p
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
geom_rsi <- function(position = NULL,
|
|
x = c("antibiotic", "interpretation"),
|
|
fill = "interpretation",
|
|
translate_ab = "name",
|
|
minimum = 30,
|
|
language = get_locale(),
|
|
combine_SI = TRUE,
|
|
combine_IR = FALSE,
|
|
...) {
|
|
x <- x[1]
|
|
stop_ifnot_installed("ggplot2")
|
|
stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
|
|
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
|
|
meet_criteria(x, allow_class = "character", has_length = 1)
|
|
meet_criteria(fill, allow_class = "character", has_length = 1)
|
|
meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
|
|
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1)
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
|
|
meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
|
|
|
|
y <- "value"
|
|
if (missing(position) | is.null(position)) {
|
|
position <- "fill"
|
|
}
|
|
|
|
if (identical(position, "fill")) {
|
|
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
|
|
}
|
|
|
|
# we work with aes_string later on
|
|
x_deparse <- deparse(substitute(x))
|
|
if (x_deparse != "x") {
|
|
x <- x_deparse
|
|
}
|
|
if (x %like% '".*"') {
|
|
x <- substr(x, 2, nchar(x) - 1)
|
|
}
|
|
|
|
if (tolower(x) %in% tolower(c("ab", "abx", "antibiotics"))) {
|
|
x <- "antibiotic"
|
|
} else if (tolower(x) %in% tolower(c("SIR", "RSI", "interpretations", "result"))) {
|
|
x <- "interpretation"
|
|
}
|
|
|
|
ggplot2::layer(geom = "bar", stat = "identity", position = position,
|
|
mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
|
|
params = list(...), data = function(x) {
|
|
rsi_df(data = x,
|
|
translate_ab = translate_ab,
|
|
language = language,
|
|
minimum = minimum,
|
|
combine_SI = combine_SI,
|
|
combine_IR = combine_IR)
|
|
})
|
|
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
|
|
facet <- facet[1]
|
|
stop_ifnot_installed("ggplot2")
|
|
meet_criteria(facet, allow_class = "character", has_length = 1)
|
|
meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE)
|
|
|
|
# we work with aes_string later on
|
|
facet_deparse <- deparse(substitute(facet))
|
|
if (facet_deparse != "facet") {
|
|
facet <- facet_deparse
|
|
}
|
|
if (facet %like% '".*"') {
|
|
facet <- substr(facet, 2, nchar(facet) - 1)
|
|
}
|
|
|
|
if (tolower(facet) %in% tolower(c("SIR", "RSI", "interpretations", "result"))) {
|
|
facet <- "interpretation"
|
|
} else if (tolower(facet) %in% tolower(c("ab", "abx", "antibiotics"))) {
|
|
facet <- "antibiotic"
|
|
}
|
|
|
|
ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
|
|
stop_ifnot_installed("ggplot2")
|
|
meet_criteria(breaks, allow_class = c("numeric", "integer"))
|
|
meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
if (all(breaks[breaks != 0] > 1)) {
|
|
breaks <- breaks / 100
|
|
}
|
|
ggplot2::scale_y_continuous(breaks = breaks,
|
|
labels = percentage(breaks),
|
|
limits = limits)
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
scale_rsi_colours <- function(colours = c(S = "#61a8ff",
|
|
SI = "#61a8ff",
|
|
I = "#61f7ff",
|
|
IR = "#ff6961",
|
|
R = "#ff6961")) {
|
|
stop_ifnot_installed("ggplot2")
|
|
meet_criteria(colours, allow_class = c("character", "logical"))
|
|
|
|
# previous colour: palette = "RdYlGn"
|
|
# previous colours: values = c("#b22222", "#ae9c20", "#7cfc00")
|
|
|
|
if (!identical(colours, FALSE)) {
|
|
original_cols <- c(S = "#61a8ff",
|
|
SI = "#61a8ff",
|
|
I = "#61f7ff",
|
|
IR = "#ff6961",
|
|
R = "#ff6961")
|
|
colours <- replace(original_cols, names(colours), colours)
|
|
ggplot2::scale_fill_manual(values = colours)
|
|
}
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
theme_rsi <- function() {
|
|
stop_ifnot_installed("ggplot2")
|
|
ggplot2::theme_minimal(base_size = 10) +
|
|
ggplot2::theme(panel.grid.major.x = ggplot2::element_blank(),
|
|
panel.grid.minor = ggplot2::element_blank(),
|
|
panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
|
|
# center title and subtitle
|
|
plot.title = ggplot2::element_text(hjust = 0.5),
|
|
plot.subtitle = ggplot2::element_text(hjust = 0.5))
|
|
}
|
|
|
|
#' @rdname ggplot_rsi
|
|
#' @export
|
|
labels_rsi_count <- function(position = NULL,
|
|
x = "antibiotic",
|
|
translate_ab = "name",
|
|
minimum = 30,
|
|
language = get_locale(),
|
|
combine_SI = TRUE,
|
|
combine_IR = FALSE,
|
|
datalabels.size = 3,
|
|
datalabels.colour = "grey15") {
|
|
stop_ifnot_installed("ggplot2")
|
|
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
|
|
meet_criteria(x, allow_class = "character", has_length = 1)
|
|
meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
|
|
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1)
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
|
|
meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
|
|
meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1)
|
|
meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
|
|
|
|
if (is.null(position)) {
|
|
position <- "fill"
|
|
}
|
|
if (identical(position, "fill")) {
|
|
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
|
|
}
|
|
x_name <- x
|
|
ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
|
|
x = x,
|
|
y = "value"),
|
|
position = position,
|
|
inherit.aes = FALSE,
|
|
size = datalabels.size,
|
|
colour = datalabels.colour,
|
|
lineheight = 0.75,
|
|
data = function(x) {
|
|
transformed <- rsi_df(data = x,
|
|
translate_ab = translate_ab,
|
|
combine_SI = combine_SI,
|
|
combine_IR = combine_IR,
|
|
minimum = minimum,
|
|
language = language)
|
|
transformed$gr <- transformed[, x_name, drop = TRUE]
|
|
transformed %pm>%
|
|
pm_group_by(gr) %pm>%
|
|
pm_mutate(lbl = paste0("n=", isolates)) %pm>%
|
|
pm_ungroup() %pm>%
|
|
pm_select(-gr)
|
|
})
|
|
}
|