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#
# ggdendro/R/dendro_tree.R by Andrie de Vries Copyright (C) 2011-2015
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
#
#' Creates dendrogram plot using ggplot.
#'
#' This is a convenience function
#'
#' @param data Either a dendro object or an object that can be coerced to class
#' dendro using the [dendro_data()] function, i.e. objects of class
#' dendrogram, hclust or tree
#'
#' @param segments If TRUE, show line segments
#'
#' @param labels if TRUE, shows segment labels
#'
#' @param leaf_labels if TRUE, shows leaf labels
#'
#' @param rotate if TRUE, rotates plot by 90 degrees
#'
#' @param theme_dendro if TRUE, applies a blank theme to plot (see
#' [theme_dendro()])
#'
#' @param ... other parameters passed to [ggplot2::geom_text()]
#'
#' @export
#' @return A [ggplot2::ggplot()] object
#' @seealso [dendro_data()]
#' @example inst/examples/example_ggdendrogram.R
ggdendrogram <- function(data,
segments = TRUE, labels = TRUE, leaf_labels = TRUE,
rotate = FALSE, theme_dendro = TRUE, ...) {
dataClass <- if (inherits(data, "dendro")) data$class else class(data)
angle <- if (dataClass %in% c("dendrogram", "hclust")) {
ifelse(rotate, 0, 90)
} else {
ifelse(rotate, 90, 0)
}
hjust <- if (dataClass %in% c("dendrogram", "hclust")) {
ifelse(rotate, 1, 1)
} else {
0.5
}
if (!is.dendro(data)) data <- dendro_data(data)
p <- ggplot() +
geom_blank()
if (segments && !is.null(data$segments)) {
p <- p + geom_segment(
data = segment(data),
aes_string(x = "x", y = "y", xend = "xend", yend = "yend")
)
}
if (leaf_labels && !is.null(data$leaf_labels)) {
p <- p + geom_text(
data = leaf_label(data),
aes_string(x = "x", y = "y", label = "label"), hjust = hjust, angle = angle, ...
)
}
if (labels) {
p <- p + scale_x_continuous(
breaks = seq_along(data$labels$label),
labels = data$labels$label
)
}
if (rotate) {
p <- p + coord_flip()
p <- p + scale_y_continuous()
} else {
p <- p + scale_y_continuous()
}
if (theme_dendro) p <- p + theme_dendro()
p <- p +
theme(axis.text.x = element_text(angle = angle, hjust = 1, vjust = 0.5)) +
theme(axis.text.y = element_text(angle = angle, hjust = 1))
p
}
#' Creates completely blank theme in ggplot.
#'
#' Sets most of the `ggplot` options to blank, by returning blank `theme`
#' elements for the panel grid, panel background, axis title, axis text, axis
#' line and axis ticks.
#' @export
theme_dendro <- function() {
element_blank <- ggplot2::element_blank
ggplot2::theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
axis.title.x = element_text(colour = NA),
axis.title.y = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.line = element_blank(),
axis.ticks = element_blank()
)
}
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