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")

Scott, I've just started investigating the ggdendro package

https://github.com/andrie/ggdendro

which appears to do many of the things you're discussing here. It doesn't yet support phylo class trees, but I'm looking into creating a dendro_data.phylo function that would solve that problem. I'll post again if I figure it out.

In the time since you posted this, have you found any other solutions to this? I want to create a specialized version of this in my package. So far ggdendro appears to be the most promising route.

By the way, I just came across this informative tag about ggplot2 in StackOverflow (mentions ggdendro):

http://stackoverflow.com/tags/ggplot2/info

Hi, gjuggler has started a ggphylo package on github, which is far better than the code in the gist above. This stuff is above my skill level, so maybe you and gjuggler can chat and make something awesome!

S

Thanks, I'll check it out!

joey