R/ggdendrogram.R

Defines functions theme_dendro ggdendrogram

Documented in ggdendrogram theme_dendro

#
#  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 \code{\link{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 \code{\link{theme_dendro}}) 
#' @param ... other parameters passed to \code{\link[ggplot2]{geom_text}}
#' @export
#' @return A \code{\link[ggplot2]{ggplot}} object
#' @seealso \code{\link{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$class else class(data)
  angle <- if(dataClass %in% c("dendrogram", "hclust")){
    ifelse(rotate, 0, 90)
  } else {
    ifelse(rotate, 90, 0)
  }
  hjust <- if(dataClass %in% c("dendrogram", "hclust")){
    ifelse(rotate, 0, 1)
  } else {
    0.5
  }
  if(!is.dendro(data)) data <- dendro_data(data)
  p <- ggplot() + geom_blank()
  if(segments && !is.null(data$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)) +
    theme(axis.text.y = element_text(angle=angle, hjust=1))
  
  p
}


#' Creates completely blank theme in ggplot.
#' 
#' Sets most of the \code{ggplot} options to blank, by returning blank \code{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()
  )
}
andrie/ggdendro documentation built on June 3, 2017, 7:02 p.m.