cytoscape.js-markov-cluster's Introduction

cytoscape-markov-cluster

A Markov Cluster (MCL) algorithm for Cytoscape.js.

Zoe Xi, for Google Summer of Code.

Dependencies

Cytoscape.js >= 2.6.12

Usage instructions

Download the library:

via npm: npm install cytoscape-markov-cluster,
via bower: bower install cytoscape-markov-cluster, or
via direct download in the repository.

require() the library as appropriate for your project:

CommonJS:

var cytoscape = require('cytoscape');
var markovCluster = require('cytoscape-markov-cluster');

markovCluster( cytoscape ); // register extension

AMD:

require(['cytoscape', 'cytoscape-markov-cluster'], function( cytoscape, markovCluster ){
  markovCluster( cytoscape ); // register extension
});

Plain HTML/JS has the extension registered for you automatically, because no require() is needed.

API

var clusters = cy.elements().markovCluster({
    expandFactor: 2,        // affects time of computation and cluster granularity to some extent: M * M
    inflateFactor: 2,       // affects cluster granularity (the greater the value, the more clusters): M(i,j) / E(j)
    multFactor: 1,          // optional self loops for each node. Use a neutral value to improve cluster computations.
    maxIterations: 10,      // maximum number of iterations of the MCL algorithm in a single run
    attributes: [           // attributes/features used to group nodes, ie. similarity values between nodes
        function(edge) {
            return edge.data('weight');
        }
        // ... and so on
     ]
});

Publishing instructions

This project is set up to automatically be published to npm and bower. To publish:

Set the version number environment variable: export VERSION=1.2.3
Publish: gulp publish
If publishing to bower for the first time, you'll need to run bower register cytoscape-markov-cluster https://github.com/cytoscape/cytoscape.js-markov-cluster.git

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