# Bioconductor Ggtree

Ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Design
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ggtree -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ggtree -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ggtree -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ggtree -g -a gemini-cli -y`

## Description

ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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.

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/genomics/ggtree/SKILL.md