A simple function for plotting phylogenies in ggplot2

UPDATE: Greg jordan has a much more elegant way of plotting trees with ggplot2. See his links in the comments below.


I wrote a simple function for plotting a phylogeny in ggplot2. However, it only handles a 3 species tree right now, as I haven't figured out how to generalize the approach to N species.

Any ideas on how to improve this?

	###### Simple function for plotting phylogenies in ggplot2
	# x = a phylo object
	# form = one of: star or ladder
	# dependencies: ape, ggplot2, adephylo (loaded within function)
	ggtree <- function(x, form) {
	# Load packages
	require(ape); require(ggplot2); require(adephylo)
	# Define plotting format
	phytheme_ <- function()
	list(theme_bw(),
	opts(panel.grid.major = theme_blank(), panel.grid.minor = theme_blank(),
	legend.position="none", axis.text.x = NULL, axis.text.y = NULL,
	axis.ticks = NULL, panel.border = NULL),
	labs(x = "", y = ""))
	# Process newick file
	tree_ <- as(as(x, "phylo4"), "data.frame") # convert to phylo4 table
	tree_tips <- tree_[tree_$node.type == "tip", ] # get table with tips only
	ntips <- nrow(tree_tips) # get number of tips
	# Plot tree
	if ( form == "ladder" ) {
	t_ <- ggplot(tree_) +
	geom_segment(aes(x = 1, y = 1, xend = 1-tree_[1,4], yend = 1)) + # tip
	geom_segment(aes(x = 1, y = 2, xend = 1-tree_[2,4], yend = 2)) + # tip
	geom_segment(aes(x = 1, y = 3, xend = 1-tree_[3,4], yend = 3)) + # tip
	geom_segment(aes(x = 1-tree_[1,4], y = 1.5, xend = 1-tree_[1,4]-tree_[5,4], yend = 1.5)) +
	geom_segment(aes(x = 1-tree_[1,4], y = 1, xend = 1-tree_[1,4], yend = 2)) +
	geom_segment(aes(x = 1-tree_[3,4], y = 1.5, xend = 1-tree_[3,4], yend = 3)) +
	geom_text(data = tree_tips, aes(x = 1, y = node, label = label, hjust = 0)) + # label tips
	phytheme_() # add theme options
	return(t_) } else # return tree
	if ( form == "star" ) {
	tree_tips_ <- cbind(tree_tips, star = seq(0, 1, 0.5)) # add column of star end locations
	star_t_ <- ggplot(tree_tips_) +
	geom_segment(aes(x = 0, y = 0.5, xend = 1, yend = tree_tips_[1,6])) + # tip
	geom_segment(aes(x = 0, y = 0.5, xend = 1, yend = tree_tips_[2,6])) + # tip
	geom_segment(aes(x = 0, y = 0.5, xend = 1, yend = tree_tips_[3,6])) + # tip
	geom_text(aes(x = 1, y = star, label = label, hjust = 0)) + # label tips
	phytheme_() # add theme options
	return(star_t_) } # return tree
	}
	###### Example
	tree <- rcoal(3)
	ggtree(tree, "star")
	ggtree(tree, "ladder")

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