mirror of https://github.com/msberends/AMR
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# ==================================================================== # |
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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 Stable Lifecycle |
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#' @inheritSection AMR Read more on Our Website! |
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#' @param x MIC values created with [as.mic()] or disk diffusion values created with [as.disk()] |
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#' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()] |
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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 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 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 expand 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 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 `ggplot` 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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#' |
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#' plot(some_mic_values) |
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#' plot(some_disk_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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#' if (require("ggplot2")) { |
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#' ggplot(some_mic_values) |
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#' ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro") |
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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 |
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#' @export |
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#' @rdname plot |
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plot.mic <- function(x, |
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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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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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expand = TRUE, |
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...) { |
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meet_criteria(main, allow_class = "character") |
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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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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_and_sub(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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...) |
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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$cols), 1.1, 1)), |
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ylab = ylab, |
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xlab = xlab, |
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axes = FALSE) |
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axis(2, seq(0, max(as.double(x)))) |
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if (!is.null(cols_sub$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 (colours_RSI[2] %in% cols_sub$cols) { |
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legend_txt <- "Susceptible" |
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legend_col <- colours_RSI[2] |
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} |
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if (colours_RSI[3] %in% cols_sub$cols) { |
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legend_txt <- c(legend_txt, "Incr. exposure") |
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legend_col <- c(legend_col, colours_RSI[3]) |
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} |
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if (colours_RSI[1] %in% cols_sub$cols) { |
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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 = legend_txt, |
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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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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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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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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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expand = TRUE, |
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...) { |
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meet_criteria(main, allow_class = "character") |
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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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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 ggplot 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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ggplot.mic <- function(data, |
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mapping = NULL, |
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title = paste("MIC values of", deparse(substitute(data))), |
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ylab = "Frequency", |
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xlab = "Minimum Inhibitory Concentration (mg/L)", |
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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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expand = TRUE, |
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...) { |
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stop_ifnot_installed("ggplot2") |
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meet_criteria(title, allow_class = "character") |
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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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title <- gsub(" +", " ", paste0(title, collapse = " ")) |
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|
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x <- plot_prepare_table(data, expand = expand) |
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cols_sub <- plot_colours_and_sub(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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...) |
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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$cols == colours_RSI[3]] <- "Incr. exposure" |
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df$cols <- factor(df$cols, |
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levels = c("Susceptible", "Incr. exposure", "Resistant"), |
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ordered = TRUE) |
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if (!is.null(mapping)) { |
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p <- ggplot2::ggplot(df, mapping = mapping) |
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} else { |
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p <- ggplot2::ggplot(df) |
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} |
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|
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if (any(colours_RSI %in% cols_sub$cols)) { |
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p <- p + |
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ggplot2::geom_col(aes(x = mic, y = count, fill = cols)) + |
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ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1], |
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"Susceptible" = colours_RSI[2], |
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"Incr. exposure" = colours_RSI[3]),, |
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name = NULL) |
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} else { |
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p <- p + |
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ggplot2::geom_col(aes(x = mic, y = count)) |
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} |
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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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|
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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 |
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#' @rdname plot |
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plot.disk <- function(x, |
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main = paste("Disk zones values 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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expand = TRUE, |
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...) { |
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meet_criteria(main, allow_class = "character") |
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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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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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|
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x <- plot_prepare_table(x, expand = expand) |
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|
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cols_sub <- plot_colours_and_sub(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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...) |
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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$sub) |
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} |
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|
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if (any(colours_RSI %in% cols_sub$cols)) { |
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legend_txt <- character(0) |
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legend_col <- character(0) |
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if (colours_RSI[1] %in% cols_sub$cols) { |
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legend_txt <- "Resistant" |
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legend_col <- colours_RSI[1] |
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} |
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if (colours_RSI[3] %in% cols_sub$cols) { |
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legend_txt <- c(legend_txt, "Incr. exposure") |
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legend_col <- c(legend_col, colours_RSI[3]) |
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} |
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if (colours_RSI[2] %in% cols_sub$cols) { |
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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 = legend_txt, |
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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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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 values 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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expand = TRUE, |
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...) { |
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meet_criteria(main, allow_class = "character") |
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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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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 ggplot 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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ggplot.disk <- function(data, |
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mapping = NULL, |
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title = paste("Disk zones values of", deparse(substitute(data))), |
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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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expand = TRUE, |
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...) { |
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stop_ifnot_installed("ggplot2") |
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meet_criteria(title, allow_class = "character") |
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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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|
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title <- gsub(" +", " ", paste0(title, collapse = " ")) |
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|
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x <- plot_prepare_table(data, expand = expand) |
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cols_sub <- plot_colours_and_sub(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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...) |
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df <- as.data.frame(x, stringsAsFactors = TRUE) |
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colnames(df) <- c("disk", "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$cols == colours_RSI[3]] <- "Incr. exposure" |
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df$cols <- factor(df$cols, |
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levels = c("Resistant", "Incr. exposure", "Susceptible"), |
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ordered = TRUE) |
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if (!is.null(mapping)) { |
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p <- ggplot2::ggplot(df, mapping = mapping) |
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} else { |
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p <- ggplot2::ggplot(df) |
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} |
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|
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if (any(colours_RSI %in% cols_sub$cols)) { |
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p <- p + |
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ggplot2::geom_col(aes(x = disk, y = count, fill = cols)) + |
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ggplot2::scale_fill_manual(values = c("Resistant" = colours_RSI[1], |
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"Susceptible" = colours_RSI[2], |
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"Incr. exposure" = colours_RSI[3]), |
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name = NULL) |
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} else { |
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p <- p + |
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ggplot2::geom_col(aes(x = disk, y = count)) |
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} |
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|
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p + |
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ggplot2::labs(title = title, x = xlab, y = ylab, sub = cols_sub$sub) |
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} |
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|
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plot_prepare_table <- function(x, expand) { |
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if (is.mic(x)) { |
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if (expand == TRUE) { |
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# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print |
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extra_range <- max(as.double(x)) / 2 |
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while (min(extra_range) / 2 > min(as.double(x))) { |
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extra_range <- c(min(extra_range) / 2, extra_range) |
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} |
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extra_range <- setNames(rep(0, length(extra_range)), extra_range) |
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x <- table(droplevels(x, as.mic = FALSE)) |
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extra_range <- extra_range[!names(extra_range) %in% names(x)] |
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x <- as.table(c(x, extra_range)) |
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} else { |
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x <- table(droplevels(x, as.mic = FALSE)) |
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} |
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x <- x[order(as.double(as.mic(names(x))))] |
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} else if (is.disk(x)) { |
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if (expand == TRUE) { |
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# expand range for disks from lowest to highest so all mm's in between also print |
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extra_range <- rep(0, max(x) - min(x) - 1) |
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names(extra_range) <- seq(min(x) + 1, max(x) - 1) |
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x <- table(x) |
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extra_range <- extra_range[!names(extra_range) %in% names(x)] |
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x <- as.table(c(x, extra_range)) |
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} else { |
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x <- table(x) |
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} |
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x <- x[order(as.double(names(x)))] |
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} |
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as.table(x) |
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} |
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|
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plot_colours_and_sub <- function(x, mo, ab, guideline, colours_RSI, fn, ...) { |
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if (!is.null(mo) && !is.null(ab)) { |
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# interpret and give colour based on MIC values |
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mo <- as.mo(mo) |
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ab <- as.ab(ab) |
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guideline <- get_guideline(guideline, AMR::rsi_translation) |
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rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...))) |
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cols <- character(length = length(rsi)) |
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cols[is.na(rsi)] <- "#BEBEBE" |
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cols[rsi == "R"] <- colours_RSI[1] |
||||
cols[rsi == "S"] <- colours_RSI[2] |
||||
cols[rsi == "I"] <- colours_RSI[3] |
||||
moname <- mo_name(mo, language = NULL) |
||||
abname <- ab_name(ab, language = NULL) |
||||
if (all(cols == "#BEBEBE")) { |
||||
message_("No ", guideline, " interpretations found for ", |
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname) |
||||
guideline <- "" |
||||
} else { |
||||
guideline <- paste0("(following ", guideline, ")") |
||||
} |
||||
sub <- bquote(.(abname)~"in"~italic(.(moname))~.(guideline)) |
||||
} else { |
||||
cols <- "#BEBEBE" |
||||
sub <- NULL |
||||
} |
||||
list(cols = 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) |
||||
|
||||
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$x, levels = c("R", "S", "I"), ordered = TRUE) |
||||
|
||||
ymax <- pm_if_else(max(data$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"), |
||||
expand = TRUE, |
||||
...) { |
||||
meet_criteria(xlab, allow_class = "character", has_length = 1) |
||||
meet_criteria(main, allow_class = "character", has_length = 1) |
||||
meet_criteria(ylab, allow_class = "character", has_length = 1) |
||||
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3)) |
||||
if (length(colours_RSI) == 1) { |
||||
colours_RSI <- rep(colours_RSI, 3) |
||||
} |
||||
main <- gsub(" +", " ", paste0(main, collapse = " ")) |
||||
|
||||
x <- table(height) |
||||
x <- x[c(3, 1, 2)] |
||||
barplot(x, |
||||
col = colours_RSI, |
||||
xlab = xlab, |
||||
main = main, |
||||
ylab = ylab, |
||||
axes = FALSE) |
||||
axis(2, seq(0, max(x))) |
||||
} |
||||
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