34  Visualising phylogenies with ggtree

Learning Objectives
  • Visualise and annotate a S. pneumoniae phylogenetic tree with the R library ggtree.

34.1 Plotting phylogenetic trees with R

Plotting phylogenetic trees with ggtree in R offers a powerful and flexible approach for visualizing evolutionary relationships. The ggtree package, built on the ggplot2 framework, enables the creation of complex and highly customizable phylogenetic tree plots. With ggtree, users can easily manipulate tree layouts, annotate nodes and branches, and incorporate additional data layers such as heatmaps or bar charts. The package supports various tree formats, including Newick, Nexus, and PhyloXML, making it versatile for different datasets. Researchers can enhance their plots with a wide array of aesthetic options, such as color coding by clade, adding tip labels, and highlighting specific evolutionary events or traits. This flexibility makes ggtree an essential tool for evolutionary biologists and bioinformaticians, facilitating the clear and informative presentation of phylogenetic data.

Exercise 1 - Plot the Pneumococcal tree with ggtree
  • Copy the preprocessed sero1.treefile to the analysis directory so that it’s in the same location as pneumo_metadata.tsv.
  • Open the script 06-plot_phylogeny.R in the scripts directory in RStudio.
  • Edit the script so it points to the sero1.treefile and pneumo_metadata.tsv files in the analysis directory.
  • Run the script to generate the annotated phylogenetic tree.
  • We copied sero1.treefile to the analysis directory:
cp preprocessed/iqtree/sero1.treefile .
  • We edited the script to point to the location of the metadata and tree files:
metadata <- read_tsv("../pneumo_metadata.tsv")

pneumo_phylogeny <- read.tree("../sero1.treefile")
  • We ran the script to generate a rooted phylogenetic tree:

Serotype 1 phylogenetic tree generated with ggtree

34.2 Summary

Key Points
  • ggtree is a highly customisable R package for generating publication quality images of phylogenetic trees.