You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

748 lines
30 KiB

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 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 data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Plotting for Classes `rsi`, `mic` and `disk`
#'
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' @inheritSection lifecycle Stable Lifecycle
#' @inheritSection AMR Read more on Our Website!
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
#' @param main,title title of the plot
#' @param xlab,ylab axis title
#' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
#' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
#' @details
#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
#'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#' @name plot
#' @rdname plot
#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
#'
#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function.
#' @param ... arguments passed on to methods
#' @examples
#' some_mic_values <- random_mic(size = 100)
#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
#' some_rsi_values <- random_rsi(50, prob_RSI = c(0.30, 0.55, 0.05))
#'
#' plot(some_mic_values)
#' plot(some_disk_values)
#' plot(some_rsi_values)
#'
#' # when providing the microorganism and antibiotic, colours will show interpretations:
#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#'
#' \donttest{
#' if (require("ggplot2")) {
#' autoplot(some_mic_values)
#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#' autoplot(some_rsi_values)
#' }
#' }
NULL
#' @method plot mic
#' @importFrom graphics barplot axis mtext legend
#' @export
#' @rdname plot
plot.mic <- function(x,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
x <- plot_prepare_table(x, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
fn = as.mic,
language = language,
...)
barplot(x,
col = cols_sub$cols,
main = main,
ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
ylab = ylab,
xlab = xlab,
axes = FALSE)
axis(2, seq(0, max(x)))
if (!is.null(cols_sub$sub)) {
mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
}
if (any(colours_RSI %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
legend_txt <- "Susceptible"
legend_col <- colours_RSI[2]
}
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
}
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Resistant")
legend_col <- c(legend_col, colours_RSI[1])
}
legend("top",
x.intersp = 0.5,
legend = translate_AMR(legend_txt, language = language),
fill = legend_col,
horiz = TRUE,
cex = 0.75,
box.lwd = 0,
box.col = "#FFFFFF55",
bg = "#FFFFFF55")
}
}
#' @method barplot mic
#' @export
#' @noRd
barplot.mic <- function(height,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
plot(x = height,
main = main,
ylab = ylab,
xlab = xlab,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
...)
}
#' @method autoplot mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.mic <- function(object,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
title = paste("MIC values of", deparse(substitute(object))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}
if (!is.null(title)) {
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
x <- plot_prepare_table(object, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
fn = as.mic,
language = language,
...)
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(translate_AMR(df$cols, language = language),
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
p <- p +
ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual(values = vals,
name = NULL,
limits = force)
} else {
p <- p +
ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
}
p +
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method fortify mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.mic <- function(object, ...) {
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
c("x", "y"))
}
#' @method plot disk
#' @export
#' @importFrom graphics barplot axis mtext legend
#' @rdname plot
plot.disk <- function(x,
main = paste("Disk zones of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
x <- plot_prepare_table(x, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
fn = as.disk,
language = language,
...)
barplot(x,
col = cols_sub$cols,
main = main,
ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
ylab = ylab,
xlab = xlab,
axes = FALSE)
axis(2, seq(0, max(x)))
if (!is.null(cols_sub$sub)) {
mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
}
if (any(colours_RSI %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
legend_txt <- "Resistant"
legend_col <- colours_RSI[1]
}
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
}
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Susceptible")
legend_col <- c(legend_col, colours_RSI[2])
}
legend("top",
x.intersp = 0.5,
legend = translate_AMR(legend_txt, language = language),
fill = legend_col,
horiz = TRUE,
cex = 0.75,
box.lwd = 0,
box.col = "#FFFFFF55",
bg = "#FFFFFF55")
}
}
#' @method barplot disk
#' @export
#' @noRd
barplot.disk <- function(height,
main = paste("Disk zones of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
plot(x = height,
main = main,
ylab = ylab,
xlab = xlab,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
...)
}
#' @method autoplot disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.disk <- function(object,
mo = NULL,
ab = NULL,
title = paste("Disk zones of", deparse(substitute(object))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}
if (!is.null(title)) {
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
x <- plot_prepare_table(object, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
fn = as.disk,
language = language,
...)
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(translate_AMR(df$cols, language = language),
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
p <- p +
ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual(values = vals,
name = NULL,
limits = force)
} else {
p <- p +
ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
}
p +
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method fortify disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.disk <- function(object, ...) {
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
c("x", "y"))
}
#' @method plot rsi
#' @export
#' @importFrom graphics plot text axis
#' @rdname plot
plot.rsi <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = paste("Resistance Overview of", deparse(substitute(x))),
...) {
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
data <- as.data.frame(table(x), stringsAsFactors = FALSE)
colnames(data) <- c("x", "n")
data$s <- round((data$n / sum(data$n)) * 100, 1)
if (!"S" %in% data$x) {
data <- rbind(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE),
stringsAsFactors = FALSE)
}
if (!"I" %in% data$x) {
data <- rbind(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE),
stringsAsFactors = FALSE)
}
if (!"R" %in% data$x) {
data <- rbind(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE),
stringsAsFactors = FALSE)
}
data$x <- factor(data$x, levels = c("S", "I", "R"), ordered = TRUE)
ymax <- pm_if_else(max(data$s) > 95, 105, 100)
plot(x = data$x,
y = data$s,
lwd = 2,
ylim = c(0, ymax),
ylab = ylab,
xlab = xlab,
main = main,
axes = FALSE)
# x axis
axis(side = 1, at = 1:pm_n_distinct(data$x), labels = levels(data$x), lwd = 0)
# y axis, 0-100%
axis(side = 2, at = seq(0, 100, 5))
text(x = data$x,
y = data$s + 4,
labels = paste0(data$s, "% (n = ", data$n, ")"))
}
#' @method barplot rsi
#' @importFrom graphics barplot axis
#' @export
#' @noRd
barplot.rsi <- function(height,
main = paste("Resistance Overview of", deparse(substitute(height))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
} else {
colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1])
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
x <- table(height)
x <- x[c(1, 2, 3)]
barplot(x,
col = colours_RSI,
xlab = xlab,
main = main,
ylab = ylab,
axes = FALSE)
axis(2, seq(0, max(x)))
}
#' @method autoplot rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.rsi <- function(object,
title = paste("Resistance Overview of", deparse(substitute(object))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}
if (!is.null(title)) {
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
}
df <- as.data.frame(table(object), stringsAsFactors = TRUE)
colnames(df) <- c("rsi", "count")
ggplot2::ggplot(df) +
ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual(values = c("R" = colours_RSI[1],
"S" = colours_RSI[2],
"I" = colours_RSI[3]),
limits = force) +
ggplot2::labs(title = title, x = xlab, y = ylab) +
ggplot2::theme(legend.position = "none")
}
#' @method fortify rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.rsi <- function(object, ...) {
stats::setNames(as.data.frame(table(object)),
c("x", "y"))
}
plot_prepare_table <- function(x, expand) {
x <- x[!is.na(x)]
stop_if(length(x) == 0, "no observations to plot", call = FALSE)
if (is.mic(x)) {
if (expand == TRUE) {
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
valid_lvls <- levels(x)
extra_range <- max(x) / 2
while (min(extra_range) / 2 > min(x)) {
extra_range <- c(min(extra_range) / 2, extra_range)
}
nms <- extra_range
extra_range <- rep(0, length(extra_range))
names(extra_range) <- nms
x <- table(droplevels(x, as.mic = FALSE))
extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
x <- as.table(c(x, extra_range))
} else {
x <- table(droplevels(x, as.mic = FALSE))
}
x <- x[order(as.double(as.mic(names(x))))]
} else if (is.disk(x)) {
if (expand == TRUE) {
# expand range for disks from lowest to highest so all mm's in between also print
extra_range <- rep(0, max(x) - min(x) - 1)
names(extra_range) <- seq(min(x) + 1, max(x) - 1)
x <- table(x)
extra_range <- extra_range[!names(extra_range) %in% names(x)]
x <- as.table(c(x, extra_range))
} else {
x <- table(x)
}
x <- x[order(as.double(names(x)))]
}
as.table(x)
}
plot_name_of_I <- function(guideline) {
if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
# interpretation since 2019
"Susceptible, incr. exp."
} else {
# interpretation until 2019
"Intermediate"
}
}
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
guideline <- get_guideline(guideline, AMR::rsi_translation)
if (!is.null(mo) && !is.null(ab)) {
# interpret and give colour based on MIC values
mo <- as.mo(mo)
ab <- as.ab(ab)
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
cols <- character(length = length(rsi))
cols[is.na(rsi)] <- "#BEBEBE"
cols[rsi == "R"] <- colours_RSI[1]
cols[rsi == "S"] <- colours_RSI[2]
cols[rsi == "I"] <- colours_RSI[3]
moname <- mo_name(mo, language = language)
abname <- ab_name(ab, language = language)
if (all(cols == "#BEBEBE")) {
message_("No ", guideline, " interpretations found for ",
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
guideline_txt <- ""
} else {
guideline_txt <- paste0("(", guideline, ")")
}
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
} else {
cols <- "#BEBEBE"
sub <- NULL
}
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
}