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(v2.1.1.9122) fix documentation
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26
R/plotting.R
26
R/plotting.R
@ -42,7 +42,10 @@
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#' @param colours_SIR colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). 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' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the package option [`AMR_locale`][AMR-options], 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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#' @param aesthetics aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"
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#' @inheritParams as.sir
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#' @inheritParams ggplot_sir
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#' @inheritParams proportion
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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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@ -80,7 +83,7 @@
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#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
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#'
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#'
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#' # Plotting using scale_x_mic()
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#' # Plotting using scale_x_mic() ---------------------------------------------
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#' \donttest{
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#' if (require("ggplot2")) {
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#' mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
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@ -120,6 +123,25 @@
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#' if (require("ggplot2")) {
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#' autoplot(some_sir_values)
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#' }
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#'
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#' # Plotting using scale_y_percent() -----------------------------------------
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#' if (require("ggplot2")) {
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#' p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
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#' counts = c(1, 1, 2, 2, 3, 3)),
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#' aes(mics, counts / sum(counts))) +
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#' geom_col()
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#' print(p)
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#'
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#' p2 <- p +
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#' scale_y_percent() +
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#' theme_sir()
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#' print(p2)
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#'
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#' p +
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#' scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
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#' limits = c(0, 1)) +
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#' theme_sir()
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#' }
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#' }
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NULL
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@ -954,7 +976,7 @@ facet_sir <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
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#' @rdname plot
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#' @export
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scale_y_percent <- function(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1), limits = NULL) {
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scale_y_percent <- function(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1), limits = c(0, NA)) {
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stop_ifnot_installed("ggplot2")
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meet_criteria(breaks, allow_class = c("numeric", "integer", "function"))
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meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
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