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724 lines
30 KiB
R
724 lines
30 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Plotting for Classes `rsi`, `mic` and `disk`
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#'
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#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
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#' @inheritSection lifecycle Maturing Lifecycle
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#' @inheritSection AMR Read more on Our Website!
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#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
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#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
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#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
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#' @param main,title title of the plot
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#' @param xlab,ylab axis title
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#' @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.
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#' @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.
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#' @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.
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#' @details
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#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
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#'
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#' 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)`.
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#'
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#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
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#' @name plot
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#' @rdname plot
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#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
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#' @param ... arguments passed on to [as.rsi()]
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#' @examples
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#' some_mic_values <- random_mic(size = 100)
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#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
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#' some_rsi_values <- random_rsi(50, prob_RSI = c(0.30, 0.55, 0.05))
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#'
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#' plot(some_mic_values)
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#' plot(some_disk_values)
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#' plot(some_rsi_values)
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#'
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#' # when providing the microorganism and antibiotic, colours will show interpretations:
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#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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#'
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#' \donttest{
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#' if (require("ggplot2")) {
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#' autoplot(some_mic_values)
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#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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#' autoplot(some_rsi_values)
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#' }
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#' }
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NULL
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#' @method plot mic
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#' @importFrom graphics barplot axis mtext legend
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#' @export
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#' @rdname plot
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plot.mic <- function(x,
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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main = paste("MIC values of", deparse(substitute(x))),
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ylab = "Frequency",
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xlab = "Minimum Inhibitory Concentration (mg/L)",
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
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language = get_locale(),
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expand = TRUE,
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...) {
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meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
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meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(ylab, allow_class = "character", has_length = 1)
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meet_criteria(xlab, allow_class = "character", has_length = 1)
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meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(expand, allow_class = "logical", has_length = 1)
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# translate if not specifically set
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if (missing(ylab)) {
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ylab <- translate_AMR(ylab, language = language)
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}
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if (missing(xlab)) {
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xlab <- translate_AMR(xlab, language = language)
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}
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if (length(colours_RSI) == 1) {
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colours_RSI <- rep(colours_RSI, 3)
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}
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main <- gsub(" +", " ", paste0(main, collapse = " "))
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x <- plot_prepare_table(x, expand = expand)
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cols_sub <- plot_colours_subtitle_guideline(x = x,
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mo = mo,
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ab = ab,
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guideline = guideline,
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colours_RSI = colours_RSI,
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fn = as.mic,
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language = language,
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...)
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barplot(x,
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col = cols_sub$cols,
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main = main,
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ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
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ylab = ylab,
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xlab = xlab,
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axes = FALSE)
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axis(2, seq(0, max(x)))
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if (!is.null(cols_sub$sub)) {
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mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
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}
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if (any(colours_RSI %in% cols_sub$cols)) {
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legend_txt <- character(0)
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legend_col <- character(0)
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if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
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legend_txt <- "Susceptible"
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legend_col <- colours_RSI[2]
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}
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if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
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legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
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legend_col <- c(legend_col, colours_RSI[3])
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}
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if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
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legend_txt <- c(legend_txt, "Resistant")
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legend_col <- c(legend_col, colours_RSI[1])
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}
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legend("top",
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x.intersp = 0.5,
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legend = translate_AMR(legend_txt, language = language),
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fill = legend_col,
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horiz = TRUE,
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cex = 0.75,
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box.lwd = 0,
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box.col = "#FFFFFF55",
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bg = "#FFFFFF55")
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}
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}
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#' @method barplot mic
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#' @export
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#' @noRd
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barplot.mic <- function(height,
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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main = paste("MIC values of", deparse(substitute(height))),
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ylab = "Frequency",
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xlab = "Minimum Inhibitory Concentration (mg/L)",
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
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language = get_locale(),
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expand = TRUE,
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...) {
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meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(ylab, allow_class = "character", has_length = 1)
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meet_criteria(xlab, allow_class = "character", has_length = 1)
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meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
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meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(expand, allow_class = "logical", has_length = 1)
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# translate if not specifically set
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if (missing(ylab)) {
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ylab <- translate_AMR(ylab, language = language)
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}
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if (missing(xlab)) {
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xlab <- translate_AMR(xlab, language = language)
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}
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main <- gsub(" +", " ", paste0(main, collapse = " "))
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plot(x = height,
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main = main,
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ylab = ylab,
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xlab = xlab,
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mo = mo,
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ab = ab,
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guideline = guideline,
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colours_RSI = colours_RSI,
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...)
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}
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#' @method autoplot mic
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#' @rdname plot
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# will be exported using s3_register() in R/zzz.R
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autoplot.mic <- function(object,
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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title = paste("MIC values of", deparse(substitute(object))),
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ylab = "Frequency",
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xlab = "Minimum Inhibitory Concentration (mg/L)",
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
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language = get_locale(),
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expand = TRUE,
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...) {
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stop_ifnot_installed("ggplot2")
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meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
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meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(ylab, allow_class = "character", has_length = 1)
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meet_criteria(xlab, allow_class = "character", has_length = 1)
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meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(expand, allow_class = "logical", has_length = 1)
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# translate if not specifically set
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if (missing(ylab)) {
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ylab <- translate_AMR(ylab, language = language)
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}
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if (missing(xlab)) {
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xlab <- translate_AMR(xlab, language = language)
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}
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if ("main" %in% names(list(...))) {
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title <- list(...)$main
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}
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if (!is.null(title)) {
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title <- gsub(" +", " ", paste0(title, collapse = " "))
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}
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x <- plot_prepare_table(object, expand = expand)
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cols_sub <- plot_colours_subtitle_guideline(x = x,
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mo = mo,
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ab = ab,
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guideline = guideline,
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colours_RSI = colours_RSI,
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fn = as.mic,
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language = language,
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...)
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df <- as.data.frame(x, stringsAsFactors = TRUE)
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colnames(df) <- c("mic", "count")
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df$cols <- cols_sub$cols
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df$cols[df$cols == colours_RSI[1]] <- "Resistant"
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df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
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df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
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df$cols <- factor(translate_AMR(df$cols, language = language),
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levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
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language = language),
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ordered = TRUE)
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p <- ggplot2::ggplot(df)
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if (any(colours_RSI %in% cols_sub$cols)) {
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vals <- c("Resistant" = colours_RSI[1],
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"Susceptible" = colours_RSI[2],
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"Susceptible, incr. exp." = colours_RSI[3],
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"Intermediate" = colours_RSI[3])
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names(vals) <- translate_AMR(names(vals), language = language)
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p <- p +
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ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
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# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
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ggplot2::scale_fill_manual(values = vals,
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name = NULL,
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limits = force)
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} else {
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p <- p +
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ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
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}
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p +
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ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
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}
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#' @method plot disk
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#' @export
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#' @importFrom graphics barplot axis mtext legend
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#' @rdname plot
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plot.disk <- function(x,
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main = paste("Disk zones of", deparse(substitute(x))),
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ylab = "Frequency",
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xlab = "Disk diffusion diameter (mm)",
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
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language = get_locale(),
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expand = TRUE,
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...) {
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meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(ylab, allow_class = "character", has_length = 1)
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meet_criteria(xlab, allow_class = "character", has_length = 1)
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meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
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meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(expand, allow_class = "logical", has_length = 1)
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# translate if not specifically set
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if (missing(ylab)) {
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ylab <- translate_AMR(ylab, language = language)
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}
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if (missing(xlab)) {
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xlab <- translate_AMR(xlab, language = language)
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}
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if (length(colours_RSI) == 1) {
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colours_RSI <- rep(colours_RSI, 3)
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}
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main <- gsub(" +", " ", paste0(main, collapse = " "))
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x <- plot_prepare_table(x, expand = expand)
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cols_sub <- plot_colours_subtitle_guideline(x = x,
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mo = mo,
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ab = ab,
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guideline = guideline,
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colours_RSI = colours_RSI,
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fn = as.disk,
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language = language,
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...)
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barplot(x,
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col = cols_sub$cols,
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main = main,
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ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
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ylab = ylab,
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xlab = xlab,
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axes = FALSE)
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axis(2, seq(0, max(x)))
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if (!is.null(cols_sub$sub)) {
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mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
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}
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if (any(colours_RSI %in% cols_sub$cols)) {
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legend_txt <- character(0)
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legend_col <- character(0)
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if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
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legend_txt <- "Resistant"
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legend_col <- colours_RSI[1]
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}
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if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
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legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
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legend_col <- c(legend_col, colours_RSI[3])
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}
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if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
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legend_txt <- c(legend_txt, "Susceptible")
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legend_col <- c(legend_col, colours_RSI[2])
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}
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legend("top",
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x.intersp = 0.5,
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legend = translate_AMR(legend_txt, language = language),
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fill = legend_col,
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horiz = TRUE,
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cex = 0.75,
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box.lwd = 0,
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box.col = "#FFFFFF55",
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bg = "#FFFFFF55")
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}
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}
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#' @method barplot disk
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#' @export
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#' @noRd
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barplot.disk <- function(height,
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main = paste("Disk zones of", deparse(substitute(height))),
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ylab = "Frequency",
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xlab = "Disk diffusion diameter (mm)",
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
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language = get_locale(),
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expand = TRUE,
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...) {
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meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(ylab, allow_class = "character", has_length = 1)
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meet_criteria(xlab, allow_class = "character", has_length = 1)
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meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
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meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(expand, allow_class = "logical", has_length = 1)
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# translate if not specifically set
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if (missing(ylab)) {
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ylab <- translate_AMR(ylab, language = language)
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}
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if (missing(xlab)) {
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xlab <- translate_AMR(xlab, language = language)
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}
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main <- gsub(" +", " ", paste0(main, collapse = " "))
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plot(x = height,
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main = main,
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ylab = ylab,
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xlab = xlab,
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mo = mo,
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ab = ab,
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guideline = guideline,
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colours_RSI = colours_RSI,
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...)
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}
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#' @method autoplot disk
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#' @rdname plot
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# 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$sub)
|
|
}
|
|
|
|
#' @method plot rsi
|
|
#' @export
|
|
#' @importFrom graphics plot text axis
|
|
#' @rdname plot
|
|
plot.rsi <- function(x,
|
|
ylab = "Percentage",
|
|
xlab = "Antimicrobial Interpretation",
|
|
main = paste("Resistance Overview of", deparse(substitute(x))),
|
|
...) {
|
|
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
|
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
|
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
|
|
|
|
data <- as.data.frame(table(x), stringsAsFactors = FALSE)
|
|
colnames(data) <- c("x", "n")
|
|
data$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")
|
|
}
|
|
|
|
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)
|
|
}
|