plot_phylo

poppr_plot_phylo.R

# Two functions to plot phylo objects from ape.
#
# Both of these functions plot their respective trees. The ... gives the user
# the ability to adjust things like color or font size. 
#
nj_plot_phylo <- function(tree, ...){
  barlen <- min(median(tree$edge.length), 0.1)
  if (barlen < 0.1) barlen <- 0.01
  tree <- ladderize(tree)
  plot.phylo(tree, font = 2, adj = 0, xpd = TRUE, 
             label.offset = 0.0125, ...)
  nodelabels(tree$node.label, adj = c(1.3, -0.5), frame = "n", cex = 0.8, 
             font = 3, xpd = TRUE)
  add.scale.bar(lwd = 5, length = barlen)
}

upgma_plot_phylo <- function(tree, ...){
  barlen <- min(median(tree$edge.length), 0.1)
  if (barlen < 0.1) barlen <- 0.01
  plot.phylo(tree, font = 2, adj = 0, xpd = TRUE, 
             label.offset = 0.0125, ...)
  nodelabels(tree$node.label, adj = c(1.3, -0.5), frame = "n", cex = 0.8, 
             font = 3, xpd = TRUE)
  axisPhylo(3)
}

usage:

devtools::source_gist("5b60cccc117276604648")
library(poppr)
# For small NJ trees
nj_plot_phylo(myNTree, cex = 0.8)
# For small UPGMA trees.
upgma_plot_phylo(myUTree, cex = 0.8)