34 Visualising phylogenies with ggtree
- 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.
34.2 Summary
- ggtree is a highly customisable R package for generating publication quality images of phylogenetic trees.