Simple function for plotting phylogenies in ggplot2

ggtree_v1.R

###### 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")

Thanks, I'll check it out!

joey