cytoscape-cola

Description

The Cola.js physics simulation layout for Cytoscape.js

The cola layout uses a force-directed physics simulation with several sophisticated constraints, written by Tim Dwyer. For more information about Cola and its parameters, refer to its documentation.

It supports noncompound and compound graphs well.

Dependencies

Cytoscape.js ^3.2.0
Cola.js ^3.1.2

Usage instructions

Download the library:

via npm: npm install cytoscape-cola,
via bower: bower install cytoscape-cola, or
via direct download in the repository (probably from a tag).

require() the library as appropriate for your project:

CommonJS:

var cytoscape = require('cytoscape');
var cycola = require('cytoscape-cola');

cytoscape.use( cycola );

AMD:

require(['cytoscape', 'cytoscape-cola', 'cola'], function( cytoscape, cycola, cola ){
  cycola( cytoscape, cola ); // register extension
});

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

API

Call the layout, e.g. cy.layout({ name: 'cola', ... }), with options:

var defaults = {
  animate: true, // whether to show the layout as it's running
  refresh: 1, // number of ticks per frame; higher is faster but more jerky
  maxSimulationTime: 4000, // max length in ms to run the layout
  ungrabifyWhileSimulating: false, // so you can't drag nodes during layout
  fit: true, // on every layout reposition of nodes, fit the viewport
  padding: 30, // padding around the simulation
  boundingBox: undefined, // constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
  nodeDimensionsIncludeLabels: undefined, // whether labels should be included in determining the space used by a node (default true)

  // layout event callbacks
  ready: function(){}, // on layoutready
  stop: function(){}, // on layoutstop

  // positioning options
  randomize: false, // use random node positions at beginning of layout
  avoidOverlap: true, // if true, prevents overlap of node bounding boxes
  handleDisconnected: true, // if true, avoids disconnected components from overlapping
  nodeSpacing: function( node ){ return 10; }, // extra spacing around nodes
  flow: undefined, // use DAG/tree flow layout if specified, e.g. { axis: 'y', minSeparation: 30 }
  alignment: undefined, // relative alignment constraints on nodes, e.g. function( node ){ return { x: 0, y: 1 } }

  // different methods of specifying edge length
  // each can be a constant numerical value or a function like `function( edge ){ return 2; }`
  edgeLength: undefined, // sets edge length directly in simulation
  edgeSymDiffLength: undefined, // symmetric diff edge length in simulation
  edgeJaccardLength: undefined, // jaccard edge length in simulation

  // iterations of cola algorithm; uses default values on undefined
  unconstrIter: undefined, // unconstrained initial layout iterations
  userConstIter: undefined, // initial layout iterations with user-specified constraints
  allConstIter: undefined, // initial layout iterations with all constraints including non-overlap

  // infinite layout options
  infinite: false // overrides all other options for a forces-all-the-time mode
};

Notes

If you want to maintain interactivity, you probably should not mix infinite: true with fit: true. Fitting naturally changes the zoom level, making dragging misaligned and feel weird to users --- though it still works technically. Better to just fit: false when infinite: true, and cy.center() or cy.fit() on layoutready.
The alignment option isn't as flexible as the raw Cola option. Here, only integers can be used to specify relative positioning, so it's a bit limited. If you'd like to see a more sophisticated implementation, please send a pull request.

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-cola https://github.com/cytoscape/cytoscape.js-cola.git
Make a release on GitHub to automatically register a new Zenodo DOI