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fix scale functions
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Package: AMR
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Version: 2.1.1.9002
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Version: 2.1.1.9003
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Date: 2023-12-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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8
NEWS.md
8
NEWS.md
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# AMR 2.1.1.9002
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# AMR 2.1.1.9003
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## Breaking
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* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents a year ago
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## New
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* Function `scale_x_mic()`, an advanced function to use in ggplot, to allow plotting of MIC values on the x axis. It allow for manual range definition and plotting missing intermediate log2 levels.
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* Function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
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* Function `rescale_mic()`, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
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### Changed
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* For MICs:
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21
R/plot.R
21
R/plot.R
@ -110,10 +110,12 @@ NULL
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#' @export
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#' @inheritParams as.mic
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#' @param drop a [logical] to remove intermediate MIC values, defaults to `FALSE`
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#' @rdname plot
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scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
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stop_ifnot_installed("ggplot2")
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scale <- ggplot2::scale_x_discrete(...)
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meet_criteria(drop, allow_class = "logical", has_length = 1)
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scale <- ggplot2::scale_x_discrete(drop = drop, ...)
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scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
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rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
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}
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@ -123,9 +125,10 @@ scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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#' @export
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#' @inheritParams as.mic
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#' @rdname plot
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scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
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stop_ifnot_installed("ggplot2")
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scale <- ggplot2::scale_y_discrete(...)
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meet_criteria(drop, allow_class = "logical", has_length = 1)
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scale <- ggplot2::scale_y_discrete(drop = drop, ...)
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scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
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rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
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}
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@ -135,9 +138,10 @@ scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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#' @export
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#' @inheritParams as.mic
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#' @rdname plot
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scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
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stop_ifnot_installed("ggplot2")
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scale <- ggplot2::scale_colour_discrete(...)
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meet_criteria(drop, allow_class = "logical", has_length = 1)
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scale <- ggplot2::scale_colour_discrete(drop = drop, ...)
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scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
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rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
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}
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@ -147,9 +151,10 @@ scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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#' @export
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#' @inheritParams as.mic
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#' @rdname plot
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scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
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scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
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stop_ifnot_installed("ggplot2")
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scale <- ggplot2::scale_fill_discrete(...)
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meet_criteria(drop, allow_class = "logical", has_length = 1)
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scale <- ggplot2::scale_fill_discrete(drop = drop, ...)
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scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
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rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
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}
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@ -27,38 +27,4 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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sir <- random_sir(100)
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rsi <- sir
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class(rsi) <- gsub("sir", "rsi", class(rsi))
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mic <- random_mic(100)
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disk <- random_disk(100)
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expect_identical(summary(sir), summary(rsi))
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expect_identical(c(sir), c(rsi))
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expect_identical(suppressWarnings(suppressMessages(as.rsi(as.character(rsi)))),
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suppressWarnings(suppressMessages(as.sir(as.character(sir)))))
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expect_identical(suppressWarnings(suppressMessages(as.rsi(mic, mo = "Escherichia coli", ab = "CIP"))),
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suppressWarnings(suppressMessages(as.sir(mic, mo = "Escherichia coli", ab = "CIP"))))
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expect_identical(suppressWarnings(suppressMessages(as.rsi(disk, mo = "Escherichia coli", ab = "CIP"))),
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suppressWarnings(suppressMessages(as.sir(disk, mo = "Escherichia coli", ab = "CIP"))))
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expect_identical(suppressWarnings(suppressMessages(as.rsi(data.frame(CIP = mic, mo = "Escherichia coli")))),
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suppressWarnings(suppressMessages(as.sir(data.frame(CIP = mic, mo = "Escherichia coli")))))
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expect_identical(suppressWarnings(n_rsi(example_isolates$CIP)),
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suppressWarnings(n_sir(example_isolates$CIP)))
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expect_identical(suppressWarnings(rsi_df(example_isolates)),
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suppressWarnings(sir_df(example_isolates)))
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expect_identical(suppressWarnings(is.rsi.eligible(example_isolates)),
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suppressWarnings(is_sir_eligible(example_isolates)))
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if (AMR:::pkg_is_available("ggplot2")) {
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expect_equal(suppressWarnings(ggplot_rsi(example_isolates[, c("CIP", "GEN", "TOB")])),
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suppressWarnings(ggplot_sir(example_isolates[, c("CIP", "GEN", "TOB")])))
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p <- ggplot2::ggplot(example_isolates[, c("CIP", "GEN", "TOB")])
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expect_equal(suppressWarnings(p + geom_rsi() + scale_rsi_colours() + labels_rsi_count() + facet_rsi() + theme_rsi()),
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suppressWarnings(p + geom_sir() + scale_sir_colours() + labels_sir_count() + facet_sir() + theme_sir()))
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}
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@ -86,10 +86,14 @@ call_functions <- c(
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"ggplot" = "ggplot2",
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"labs" = "ggplot2",
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"layer" = "ggplot2",
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"position_fill" = "ggplot2",
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"position_dodge2" = "ggplot2",
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"position_fill" = "ggplot2",
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"scale_colour_discrete" = "ggplot2",
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"scale_fill_discrete" = "ggplot2",
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"scale_fill_manual" = "ggplot2",
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"scale_x_discrete" = "ggplot2",
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"scale_y_continuous" = "ggplot2",
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"scale_y_discrete" = "ggplot2",
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"theme" = "ggplot2",
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"theme_minimal" = "ggplot2",
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"unit" = "ggplot2",
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@ -127,7 +131,7 @@ for (i in seq_len(length(import_functions))) {
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expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
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info = paste0("does not exist (anymore): function `", pkg, "::", fn, "()`")
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)
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} else {
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} else if (pkg != "rstudioapi") {
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warning("Package '", pkg, "' does not exist anymore")
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}
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}
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@ -140,3 +144,12 @@ if (AMR:::pkg_is_available("cli")) {
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if (AMR:::pkg_is_available("cli")) {
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expect_true(!is.null(cli::symbol$ellipsis))
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}
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if (AMR:::pkg_is_available("ggplot2")) {
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# the scale_*_mic() functions rely on these
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expect_true(is.function(ggplot2::scale_x_discrete()$transform))
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expect_true(is.function(ggplot2::scale_y_discrete()$transform))
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expect_true(is.function(ggplot2::scale_colour_discrete()$transform))
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expect_true(is.function(ggplot2::scale_fill_discrete()$transform))
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}
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10
man/plot.Rd
10
man/plot.Rd
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\alias{fortify.sir}
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\title{Plotting for Classes \code{sir}, \code{mic} and \code{disk}}
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\usage{
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scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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\method{plot}{mic}(
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x,
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@ -119,6 +119,8 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
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\item{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
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\item{...}{arguments passed on to methods}
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\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
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