pyclustree

Visualize cluster assignments at different resolutions. Possbile applications include finding the optimal resolution for single-cell RNA-sequencing clusterings.

pyclustree is inspired by the R package clustree (Github repository), however, while we aim to provide the same functionality, the API will differ between the implementations.

Getting started

Please refer to the documentation.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install pyclustree:

1. Install the latest release of pyclustree from PyPI:

pip install pyclustree

2. Install the latest development version:

pip install git+https://github.com/complextissue/pyclustree.git@dev

Contact

If you found a bug, please use the issue tracker.

Authors

@maltekuehl @harryhaller001

Unaffiliated with the creators of the R package clustree.

License

Please refer to the LICENSE file.

Citation

Please cite both the original R package as well as this implementation when using pyclustree. For example: Cluster resolution was determined based on visualization with pyclustree (Kuehl et al., 2024), a Python implementation of clustree (Zappia et al., 2018).

• pyclustree: Kuehl, M., Hellmig, M., & Puelles, V. G. (2024). pyclustree: Visualizing cluster resolution optimization for biomedical data (0.3.1). Zenodo. https://doi.org/10.5281/zenodo.13987570
• clustree: Zappia, L., & Oshlack, A. (2018). Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience, 7(7), giy083.