MiqG / leiden_clustering

Cluster your data matrix with the Leiden algorithm.

leiden_clustering

Description

Class wrapper based on scanpy to use the Leiden algorithm to directly cluster your data matrix with a scikit-learn flavor.

Requirements

Developed using:

• scanpy v1.7.2
• sklearn v0.23.2
• umap v0.4.6
• numpy v1.19.2
• leidenalg

Installation

pip

pip install leiden_clustering

local

git clone https://github.com/MiqG/leiden_clustering.git
cd leiden_clustering
pip install -e .

Usage

from leiden_clustering import LeidenClustering
import numpy as np
X = np.random.randn(100,10)
clustering = LeidenClustering()
clustering.fit(X)
clustering.labels_

License

leiden_clsutering is distributed under a BSD 3-Clause License (see LICENSE).

References

• Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep 9, 5233 (2019). DOI: https://doi.org/10.1038/s41598-019-41695-z