treescales.R

library(ape)
library(ggtree) ## Ggtree is on github, devtools::install_github("GuangchuangYu/ggtree")
library(ggplot2)
library(gridExtra)

## Random tree
set.seed(5)
phy <- rtree(15)

## No transformation
p1 <- ggtree(phy, ladderize = TRUE) + theme_tree2() + geom_tiplab() + ggtitle("No transform")

## Manipulate the plotting coordinates, square transform
p2 <- ggtree(phy, ladderize = TRUE) + 
  theme_tree2() + 
  geom_tiplab() + scale_x_continuous(labels = function(x) sqrt(x), breaks = seq(0, 4)^2) +  ## Backtransform the axis labels, and add appropriate breaks
  ggtitle("Square transform") 
p2$data$x <- p2$data$x ^2

## Exponential instead
p3 <- ggtree(phy, ladderize = TRUE) +
  theme_tree2() + 
  geom_tiplab() + 
  scale_x_continuous(labels = function(x) log(x), breaks = exp(seq(0, 4))) + 
  ggtitle("Exponential transform")
p3$data$x <- exp(p3$data$x)

grid.arrange(p1, p2, p3)

how about something like:

p1 + scale_x_continuous(trans='log2')