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# External facing functions -----------------------------------------------
#' @name scale_dendrogram
#' @title Dendrogram position scales
#'
#' @description
#' When discrete data has some inherent hierarchy to the relationship between
#' discrete categories, you can display a dendrogram instead of a tick axis.
#'
#' @inheritParams ggplot2::scale_x_discrete
#' @inheritDotParams ggplot2::discrete_scale -breaks
#' @param hclust An object of the type produced by the
#' [stats::hclust()] function.
#'
#' @details The dendrogram type of scale does two things, first it reorders the
#' values along the relevant direction such that they follow the order
#' captured in the `hclust` argument. Secondly, it draws the dendrogram
#' at the axis. The dendrogram visuals inherit from the ticks theme elements,
#' so defining a linetype for the tick marks sets the linetype for the
#' dendrogram.
#'
#' @export
#'
#' @return A *ScaleDendrogram* ggproto object.
#'
#' @examples
#' # Hierarchically cluster USArrests
#' yclus <- hclust(dist(USArrests), "ave")
#' xclus <- hclust(dist(t(USArrests)), "ave")
#'
#' # Melting USArrests
#' df <- data.frame(
#' State = rownames(USArrests)[row(USArrests)],
#' variable = colnames(USArrests)[col(USArrests)],
#' value = unname(do.call(c, USArrests))
#' )
#'
#' # Supply the clustering to the scales
#' ggplot(df, aes(variable, State, fill = value)) +
#' geom_raster() +
#' scale_y_dendrogram(hclust = yclus) +
#' scale_x_dendrogram(hclust = xclus)
scale_x_dendrogram <- function(...,
hclust = waiver(),
expand = waiver(),
guide = waiver(),
position = "bottom") {
# Do regular discrete axis if no hclust is provided
if (!inherits(hclust, "hclust")) {
return(scale_x_discrete(...,
expand = expand,
guide = "axis",
position = position))
}
# Set guide to dendrogram and fill dendrogram data
if (inherits(guide, "waiver") || is.character(guide) && guide == "dendro") {
guide <- guide_dendro()
}
if (inherits(guide, "guide") && inherits(guide, "dendroguide")) {
if (inherits(guide$dendro, "waiver")) {
check_installed("ggdendro", "for `scale_x_dendrogram()`.")
guide$dendro <- ggdendro::dendro_data(hclust)
}
}
# Build scale
scale_name <- if (new_guide_system) missing_arg() else "position_d"
sc <- discrete_scale(c("x", "xmin", "xmax", "xend"),
scale_name,
identity,
...,
expand = expand,
guide = guide,
position = position,
super = ScaleDendrogram)
sc$range_c <- ContinuousRange$new()
sc$hclust <- hclust
sc
}
#' @rdname scale_dendrogram
#' @export
scale_y_dendrogram <- function(...,
hclust = waiver(),
expand = waiver(),
guide = waiver(),
position = "left") {
# Do regular discrete axis if no hclust is provided
if (!inherits(hclust, "hclust")) {
return(scale_y_discrete(...,
expand = expand,
guide = "axis",
position = position))
}
# Set guide to dendrogram and fill dendrogram data
if (inherits(guide, "waiver") || is.character(guide) && guide == "dendro") {
guide <- guide_dendro()
}
if (inherits(guide, "guide") && inherits(guide, "dendroguide")) {
if (inherits(guide$dendro, "waiver")) {
check_installed("ggdendro", "for `scale_y_dendrogram()`.")
guide$dendro <- ggdendro::dendro_data(hclust)
}
}
# Build scale
scale_name <- if (new_guide_system) missing_arg() else "position_d"
sc <- discrete_scale(c("y", "ymin", "ymax", "yend"),
scale_name,
identity,
...,
expand = expand,
guide = guide,
position = position,
super = ScaleDendrogram)
sc$range_c <- ContinuousRange$new()
sc$hclust <- hclust
sc
}
# ggproto -----------------------------------------------------------------
#' @usage NULL
#' @format NULL
#' @export
#' @rdname ggh4x_extensions
ScaleDendrogram <- ggproto(
"ScaleDendrogram", ScaleDiscretePosition,
hclust = waiver(),
trans = list(), # To not trigger transformation skipping
transform = function(self, x) {
hclust <- self$hclust
if (!inherits(hclust, "waiver") && inherits(hclust, "hclust")) {
if (length(hclust$labels) != length(hclust$order)) {
cli::cli_abort(c(
"{.arg hclust} must have as many labels as there are items.",
i = "There are {length(hclust$labels)} labels.",
i = "There are {length(hclust$order)} items."
))
}
ref <- hclust$labels[hclust$order]
if (is.factor(x)) {
x <- as.character(x)
}
if (is.character(x)) {
x <- factor(x, levels = ref)
}
}
return(x)
})
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