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https://github.com/msberends/AMR.git
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new ggplot enhancement
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# Generated by using Rcpp::compileAttributes() -> do not edit by hand
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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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rsi_calc_S <- function(x, include_I) {
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.Call(`_AMR_rsi_calc_S`, x, include_I)
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}
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rsi_calc_I <- function(x) {
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.Call(`_AMR_rsi_calc_I`, x)
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}
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rsi_calc_R <- function(x, include_I) {
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.Call(`_AMR_rsi_calc_R`, x, include_I)
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}
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130
R/ggplot_rsi.R
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130
R/ggplot_rsi.R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' AMR bar plots with \code{ggplot}
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#'
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#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link{ggplot}} functions.
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#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
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#' @param position position adjustment of bars, either \code{"stack"} (default) or \code{"dodge"}
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#' @param x parameter to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"}
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#' @param facet parameter to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"}
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#' @details At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.
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#'
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#' \strong{The functions}\cr
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#' \code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{\link{portion_df}} and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
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#'
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#' \code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link{facet_wrap}}.
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#'
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#' \code{scale_y_percent} transforms the y axis to a 0 to 100% range.
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#'
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#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.
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#'
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#' \code{theme_rsi} is a \code{\link{theme}} with minimal distraction.
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#'
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#' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
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#' @rdname ggplot_rsi
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#' @export
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#' @examples
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#' library(dplyr)
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#' library(ggplot2)
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#'
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#' # get antimicrobial results for drugs against a UTI:
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#' ggplot(septic_patients %>% select(amox, nitr, fosf, trim, cipr)) +
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#' geom_rsi()
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#'
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#' # prettify it using some additional functions
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#' df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
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#' ggplot(df) +
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#' geom_rsi(x = "Interpretation") +
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#' facet_rsi(facet = "Antibiotic") +
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#' scale_y_percent() +
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#' scale_rsi_colours() +
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#' theme_rsi()
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#'
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#' # or better yet, simplify this using the wrapper function - a single command:
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#' septic_patients %>%
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#' select(amox, nitr, fosf, trim, cipr) %>%
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#' ggplot_rsi()
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#'
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#' septic_patients %>%
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#' select(amox, nitr, fosf, trim, cipr) %>%
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#' ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
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ggplot_rsi <- function(data,
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x = "Antibiotic",
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facet = NULL) {
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p <- ggplot2::ggplot(data = data) +
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geom_rsi(x = x) +
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scale_y_percent() +
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scale_rsi_colours() +
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theme_rsi()
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if (!is.null(facet)) {
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p <- p + facet_rsi(facet = facet)
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}
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p
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}
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#' @rdname ggplot_rsi
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#' @export
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geom_rsi <- function(position = "stack", x = c("Antibiotic", "Interpretation")) {
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x <- x[1]
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if (!x %in% c("Antibiotic", "Interpretation")) {
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stop("`x` must be 'Antibiotic' or 'Interpretation'")
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}
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ggplot2::layer(geom = "bar", stat = "identity", position = position,
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mapping = ggplot2::aes_string(x = x, y = "Percentage", fill = "Interpretation"),
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data = AMR::portion_df, params = list())
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}
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#' @rdname ggplot_rsi
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#' @export
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facet_rsi <- function(facet = c("Interpretation", "Antibiotic")) {
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facet <- facet[1]
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if (!facet %in% c("Antibiotic", "Interpretation")) {
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stop("`facet` must be 'Antibiotic' or 'Interpretation'")
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}
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ggplot2::facet_wrap(facets = facet, scales = "free")
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}
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#' @rdname ggplot_rsi
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#' @export
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scale_y_percent <- function() {
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ggplot2::scale_y_continuous(name = "Percentage",
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breaks = seq(0, 1, 0.1),
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limits = c(0, 1),
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labels = percent(seq(0, 1, 0.1)))
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}
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#' @rdname ggplot_rsi
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#' @export
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scale_rsi_colours <- function() {
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ggplot2::scale_fill_brewer(palette = "RdYlGn")
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}
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#' @rdname ggplot_rsi
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#' @export
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theme_rsi <- function() {
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theme_minimal() +
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theme(panel.grid.major.x = element_blank(),
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panel.grid.minor = element_blank(),
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panel.grid.major.y = element_line(colour = "grey75"))
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}
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@ -17,6 +17,14 @@
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# ==================================================================== #
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globalVariables(c('abname',
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'Antibiotic',
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'Interpretation',
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'Percentage',
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'bind_rows',
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'element_blank',
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'element_line',
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'theme',
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'theme_minimal',
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'antibiotic',
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'antibiotics',
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'atc',
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36
R/portion.R
36
R/portion.R
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#' @param ab2 like \code{ab}, a vector of antibiotic interpretations. Use this to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
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#' @param minimum minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA}. The default number of \code{30} isolates is advised by the CLSI as best practice, see Source.
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#' @param as_percent logical to indicate whether the output must be returned as percent (text), will else be a double
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#' @param data a code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})
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#' @param translate a logical value to indicate whether antibiotic abbreviations should be translated with \code{\link{abname}}
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#' @details \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
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#'
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#' \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \code{data.frame} will have three rows (for R/I/S) and a column for each variable with class \code{"rsi"}.
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#'
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#' The old \code{\link{rsi}} function is still available for backwards compatibility but is deprecated.
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#' \if{html}{
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#' \cr\cr
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@ -225,11 +229,11 @@ rsi_calc <- function(type,
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}
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if (type == "S") {
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found <- .Call(`_AMR_rsi_calc_S`, x, include_I)
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found <- sum(as.integer(x) <= 1 + include_I, na.rm = TRUE)
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} else if (type == "I") {
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found <- .Call(`_AMR_rsi_calc_I`, x)
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found <- sum(as.integer(x) == 2, na.rm = TRUE)
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} else if (type == "R") {
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found <- .Call(`_AMR_rsi_calc_R`, x, include_I)
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found <- sum(as.integer(x) >= 3 - include_I, na.rm = TRUE)
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} else {
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stop("invalid type")
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}
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found / total
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}
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}
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#' @rdname portion
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#' @importFrom dplyr bind_cols summarise_if mutate
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#' @export
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portion_df <- function(data, translate = getOption("get_antibiotic_names", TRUE)) {
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resS <- bind_cols(data.frame(Interpretation = "S", stringsAsFactors = FALSE),
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summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = portion_S))
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resI <- bind_cols(data.frame(Interpretation = "I", stringsAsFactors = FALSE),
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summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = portion_I))
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resR <- bind_cols(data.frame(Interpretation = "R", stringsAsFactors = FALSE),
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summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = portion_R))
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res <- bind_rows(resS, resI, resR) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
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tidyr::gather(Antibiotic, Percentage, -Interpretation)
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if (translate == TRUE) {
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res <- res %>% mutate(Antibiotic = abname(Antibiotic, from = "guess", to = "official"))
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}
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res
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}
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