R/ggdendrogram.R

In ggdendro: Create Dendrograms and Tree Diagrams Using 'ggplot2'

#
#  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(x = .data[["x"]], y = .data[["y"]], xend = .data[["xend"]], yend = .data[["yend"]])
    )
  }
  if (leaf_labels && !is.null(data$leaf_labels)) {
    p <- p + geom_text(
      data = leaf_label(data),
      aes(x = .data[["x"]], y = .data[["y"]], label = .data[["label"]]), hjust = hjust, angle = angle, ...
    )
  }
  if (labels) {
    p <- p + scale_x_continuous(
      breaks = seq_along(data$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()
  )
}