The heattree R package

This package makes it easy to visualize, manipulate, and export phylogenetic trees in R using an interactive viewer/editor. You can insert this tree viewer into Rmd/Quarto documents make your trees accessible online. If you want to use this for web development outside of R, consider the javascript heat-tree package which this package builds upon.

Installation

For now, heattree is only available on Github and can be installed with devtools:

devtools::install_github('grunwaldlab/heattree')

Quick start

The package includes example data sets that are automatically loaded with the package (e.g. weisberg_2020_mlsa), so you can try it out with minimal effort. After installing the packages, simply run the lines below to get an idea of how it works:

library(heattree)
heat_tree(
  tree = weisberg_2020_mlsa,
  metadata = weisberg_2020_metadata,
  aesthetics = c(tipLabelColor = 'host_type'),
  layout = 'circular')

See the “Getting Started” page for interactive examples

For Python / Jupyter Notebook users

For the python version of this package see this documentation.

For JavaScript users

For the JavaScript library that is the foundation of this package see this documentation.

Contributing and feedback

Contributions and feedback are welcome! Please visit the GitHub repository to report issues or submit pull requests.