motifcluster
A software package for motif-based spectral clustering of weighted directed networks.
First written for my master’s thesis under Mihai Cucuringu at the Department of Statistics, University of Oxford, motifcluster was further developed alongside a preprint (arXiv:2004.01293) authored by W. G. Underwood, A. Elliott, and M. Cucuringu. It is available on GitHub for R and Python.
The motifcluster packages for R and Python provide the capability for:
- Building motif adjacency matrices
- Sampling random weighted directed networks
- Spectral embedding with motif adjacency matrices
- Motif-based spectral clustering
The methods are all designed to run quickly on large sparse networks, and are easy to install and use.
R package
The motifcluster package was originally written in R.
Installation
The R package can be installed from CRAN with:
Documentation
The package’s manual is in the R/doc directory on GitHub. An instructional vignette is in the R/vignettes directory on GitHub.
Python
The motifcluster package is now also available in Python. This offers some improved performance over the R package, though the functionality is the same.
Installation
The Python package can be installed from PyPI with:
Documentation
Full documentation is available at motifcluster.readthedocs.io.