PhyloGeoPlot

PhyloGeoPlot is a Python package for linked visualization of phylogenetic trees and geographic occurrence data. It connects taxa represented in a phylogenetic tree to their geographic locations on a map and can optionally incorporate environmental raster data and quantitative trait information.

PhyloGeoPlot example

Installation

Install from PyPI:

pip install phylogeoplot

PhyloGeoPlot requires Python 3.10 or later.

Dependencies

Main dependencies are installed automatically with pip:

Biopython
Cartopy
Rasterio
Matplotlib
Pandas
NumPy
scikit-image

Basic usage

from phylogeoplot.visualisation.tree_to_map_raster import PhyloGeoPlotter

plotter = PhyloGeoPlotter(
    nwk_file="sequences_tree.nwk",
    gps_file="coordinates.csv",
    offset_file="offsets.csv",
    raster_file="environment.tif",
    raster_band=1,
)

plotter.plot()
plotter.save(output_dir="output")

Raster input is optional.

Documentation

Detailed documentation is available in the PhyloGeoPlot Wiki.

Useful pages:

Examples

The repository contains sample datasets and walkthrough notebooks for:

Malagasy Coffea
North Atlantic Cumacea

See the Examples page for details.

Source code

Source code and example data are available on GitHub:

https://github.com/tahiri-lab/PhyloGeoPlot

Tests

Run the test suite with:

python -m pytest -v

License

PhyloGeoPlot is distributed under the MIT License.

Author

Caroline Fortier

Citation

Citation information will be added here following publication.

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