https://github.com/wgunderwood/motifcluster

Motif-based weighted spectral clustering in Python, R and Julia
https://github.com/wgunderwood/motifcluster

Last synced: about 1 month ago
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Motif-based weighted spectral clustering in Python, R and Julia

• Host: GitHub
• URL: https://github.com/wgunderwood/motifcluster
• Owner: WGUNDERWOOD
• License: gpl-3.0
• Created: 2020-03-21T15:42:10.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2024-06-20T14:10:43.000Z (7 months ago)
• Last Synced: 2024-11-08T13:49:27.336Z (3 months ago)
• Language: Python
• Homepage:
• Size: 6.67 MB
• Stars: 25
• Watchers: 5
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        


# motifcluster 

Motif-based spectral clustering of weighted directed networks

[![CI](https://github.com/WGUNDERWOOD/motifcluster/actions/workflows/CI.yml/badge.svg)](https://github.com/WGUNDERWOOD/motifcluster/actions/workflows/CI.yml)

[![license: GPLv3](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

[![codecov](https://codecov.io/gh/WGUNDERWOOD/motifcluster/branch/main/graph/badge.svg?token=DbGSOsocw6)](https://codecov.io/gh/WGUNDERWOOD/motifcluster)

[![python docs](https://img.shields.io/readthedocs/motifcluster?label=python%20docs)](https://motifcluster.readthedocs.io/en/latest/)

[![R docs](https://img.shields.io/readthedocs/motifcluster?label=R%20docs)](https://github.com/WGUNDERWOOD/motifcluster/tree/main/R/doc)

[![Julia docs](https://img.shields.io/readthedocs/motifcluster?label=Julia%20docs)](https://wgunderwood.github.io/motifcluster/stable/)

## Introduction

This repository provides implementations of motif-based spectral clustering

of weighted directed networks in R, Python and Julia.

This code is based on methods detailed in

[Underwood, Elliott and Cucuringu, 2020],

which is available at

[arXiv:2004.01293](https://arxiv.org/abs/2004.01293).

These packages 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.

### Branches

The main branch contains stable versions.

The develop branch may be unstable,

and is for development purposes only.

### Authors

  - [William George Underwood](https://wgunderwood.github.io/),

    Princeton University

    (Python, R, Julia, maintainer)

  - [Andrew Elliott](https://www.turing.ac.uk/people/researchers/andrew-elliott),

    The Alan Turing Institute

    (Python)

### License

This repository

and its included R, Python and Julia packages

are all licensed under

[GPLv3](http://gplv3.fsf.org/).

## R package

The **motifcluster** R package is in the

[R](https://github.com/WGUNDERWOOD/motifcluster/tree/main/R)

directory.

### Installation

The R package can be installed from CRAN with:

```

install.packages("motifcluster")

```

### Dependencies

The R package has the following dependencies, available on CRAN:

- igraph

- Matrix

- RSpectra

### Documentation

The package's manual is in the

[R/doc](https://github.com/WGUNDERWOOD/motifcluster/tree/main/R/doc)

directory.

R documentation files are provided for each function

available in the package.

An instructional vignette is in the

[R/vignettes](https://github.com/WGUNDERWOOD/motifcluster/tree/main/R/vignettes)

directory.

## Python package

The **motifcluster** Python package is in the

[python](https://github.com/WGUNDERWOOD/motifcluster/tree/main/python)

directory.

### Installation

The Python package can be installed from PyPI with:

```

pip install motifcluster

```

Alternatively it can be installed with conda using:

```

conda install -c conda-forge motifcluster

```

### Dependencies

The Python package has the following dependencies:

- Networkx

- Numpy

- Scipy

- Scikit-learn

### Documentation

Full documentation is available at

[motifcluster.readthedocs.io](https://motifcluster.readthedocs.io/).

## Julia package

The **MotifCluster** Julia package is in the

[julia](https://github.com/WGUNDERWOOD/motifcluster/tree/main/julia)

directory.

### Installation

From the Julia General registry:

```

] add MotifCluster

```

### Dependencies

- Aqua

- Clustering

- Distributions

- Graphs

### Documentation

Documentation for the **MotifCluster** package is available on 

[the web](https://wgunderwood.github.io/motifcluster/stable/).

## Performance

The

[performance](https://github.com/WGUNDERWOOD/motifcluster/tree/main/performance)

directory contains scripts and plots relating to timing

the construction of motif adjacency matrices,

in R, Python and Julia.

## Sticker

A high-resolution hexagonal sticker is available in the

[sticker](https://github.com/WGUNDERWOOD/motifcluster/tree/main/sticker)

directory.