ggtree

ggtree extends the ggplot2 plotting system to implement the grammar of graphics for phylogenetic trees. It is designed for the visualization, manipulation, and annotation of phylogenetic trees and other tree-like structures with their associated multi-omics and clinical metadata.

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 4.2.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: ape, aplot, cli, dplyr, ggfun, ggiraph, ggplot2, magrittr, purrr, rlang, scales, tidyr, tidytree, treeio, yulab.utils
• Install: BiocManager::install("ggtree")

When to Use

• Visualizing complex phylogenetic trees (e.g., from RAxML, IQ-TREE, or BEAST) integrated with multi-omics metadata (such as microbiome abundance, genomic features, or clinical traits).
• Annotating tree nodes, clades, and leaves with custom shapes, colors, images, or subplots (e.g., barplots, pie charts) using the grammar of graphics.
• Displaying circular, radial, rectangular, or slanted tree layouts for large-scale evolutionary studies containing hundreds to thousands of taxa.

When NOT to Use

• For interactive, web-based tree exploration, use phylocanvas or iTOL instead because ggtree produces static vector graphics.
• For simple, quick tree plotting without complex annotations, use ape::plot.phylo instead because it has zero overhead and requires no ggplot2 syntax.
• For highly customized interactive network visualizations that are not strictly hierarchical, use ggnetwork or tidygraph instead because ggtree is optimized specifically for tree topologies.