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(v1.7.1.9053) fortify() methods

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dr. M.S. (Matthijs) Berends
2021-11-01 13:51:13 +01:00
parent 91149d6d35
commit 9a2c431e16
25 changed files with 1046 additions and 965 deletions
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29
R/plot.R
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@ -28,7 +28,7 @@
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' @inheritSection lifecycle Maturing Lifecycle
#' @inheritSection AMR Read more on Our Website!
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
@ -46,7 +46,9 @@
#' @name plot
#' @rdname plot
#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
#' @param ... arguments passed on to [as.rsi()]
#'
#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function.
#' @param ... arguments passed on to methods
#' @examples
#' some_mic_values <- random_mic(size = 100)
#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
@ -283,6 +285,13 @@ autoplot.mic <- function(object,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method fortify mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.mic <- function(object, ...) {
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
c("x", "y"))
}
#' @method plot disk
#' @export
@ -500,6 +509,14 @@ autoplot.disk <- function(object,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$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
@ -646,6 +663,14 @@ autoplot.rsi <- function(object,
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)