Visualizing trees of many genes quickly with ggtree

Once you have computed a tree, the first thing you will want to do with it is take a look. That’s possible in many programs, but R has an extremely powerful, flexible, and fast system in the form of the ggtree package. In this recipe, we’ll learn how to get into ggtree and re-layout, highlight, and annotate tree images in just a few commands.

Getting ready

You’ll need the ggplot2, ggtree, and ape packages. You’ll also require the itol.nwk file from the rbioinfcookbook package. The file is a Newick tree of 191 species from the Interactive Tree of Life online tool’s public dataset. At the time of writing, there is an issue with an upstream dependency that causes this code to fail, though it is correct. We hope this will have gone away by the time you read this. If it hasn’t, a workaround is to install the source version of ggtree from Biocmanager, like this:

BiocManager::install("...