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749 lines
30 KiB
749 lines
30 KiB
# ==================================================================== # |
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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) 2018-2022 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 Stable 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()] (or their `random_*` variants, such as [random_mic()]) |
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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_AMR_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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#' |
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#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function. |
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#' @param ... arguments passed on to methods |
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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_AMR_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_AMR_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_AMR_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 fortify 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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fortify.mic <- function(object, ...) { |
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stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)), |
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c("x", "y")) |
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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_AMR_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_AMR_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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|
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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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|
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main <- gsub(" +", " ", paste0(main, collapse = " ")) |
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|
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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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|
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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 |
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autoplot.disk <- function(object, |
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mo = NULL, |
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ab = NULL, |
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title = paste("Disk zones of", deparse(substitute(object))), |
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ylab = "Frequency", |
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xlab = "Disk diffusion diameter (mm)", |
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guideline = "EUCAST", |
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colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"), |
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language = get_AMR_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(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(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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|
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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(...))) { |
|
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_AMR_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_AMR_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) |
|
}
|
|
|