Examples

Example datasets and walkthroughs

Complete walkthrough notebooks and sample datasets are available in the GitHub repository:

PhyloGeoPlot GitHub repository

The repository currently includes two principal use cases.

Use case 1 – Malagasy Coffea

This example links a phylogenetic tree of Malagasy Coffea taxa to specimen occurrence records in Madagascar.

Trait values such as caffeine concentration can be represented using a continuous color scale, and environmental raster layers can be included in the geographic panel.

Example notebooks:

• PhyloGeoPlot walkthrough
• Tree-to-map raster walkthrough

Sample data are available under:

examples/sample_data/use_case_1/

Use case 2 – North Atlantic Cumacea

This example illustrates linked phylogenetic and geographic visualization for Cumacea taxa distributed across North Atlantic regions.

Example notebook:

• Cumacea tree-to-map walkthrough

Sample data are available under:

examples/sample_data/use_case_2/

Running the repository examples

The example datasets and notebooks are maintained in the GitHub repository and are not bundled into the PyPI installation.

To reproduce the examples, clone the repository:

git clone https://github.com/tahiri-lab/PhyloGeoPlot.git
cd PhyloGeoPlot

Install the package in editable mode with the development dependencies:

pip install -e ".[dev]"

The example files can then be accessed under:

examples/
├── sample_data/
│   ├── use_case_1/
│   └── use_case_2/
├── use_case_1/
└── use_case_2/

For example:

python -m phylogeoplot.preprocessing.format_gbif_data \
    examples/sample_data/use_case_1/gbif_coffea_ex3.csv \
    examples/sample_data/use_case_1/node_names.csv