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 data 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 datasets/ch4 folder of this book's repository, which is a Newick tree of 191 species from the Interactive Tree of Life online tool's public dataset.

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