The Cola.js physics simulation layout for Cytoscape.js
npm install cytoscape-colacytoscape-cola
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The Cola.js physics simulation layout for Cytoscape.js (demo, non-animated demo, compound demo, constraint demo)
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.
* Cytoscape.js ^3.2.0
* Cola.js ^3.1.2
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).
Import the library as appropriate for your project:
ES import:
``js
import cytoscape from 'cytoscape';
import cola from 'cytoscape-cola';
cytoscape.use( cola );
`
CommonJS require:
`js
let cytoscape = require('cytoscape');
let cola = require('cytoscape-cola');
cytoscape.use( cola ); // register extension
`
AMD:
`js`
require(['cytoscape', 'cytoscape-cola'], function( cytoscape, cola ){
cola( cytoscape ); // register extension
});
Plain HTML/JS has the extension registered for you automatically, because no require() is needed.
Call the layout, e.g. cy.layout({ name: 'cola', ... }), with options:
`js
// default layout 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: false, // whether labels should be included in determining the space used by a node
// 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
convergenceThreshold: 0.01, // when the alpha value (system energy) falls below this value, the layout stops
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. {vertical: [[{node: node1, offset: 0}, {node: node2, offset: 5}]], horizontal: [[{node: node3}, {node: node4}], [{node: node5}, {node: node6}]]}
gapInequalities: undefined, // list of inequality constraints for the gap between the nodes, e.g. [{"axis":"y", "left":node1, "right":node2, "gap":25}]
centerGraph: true, // adjusts the node positions initially to center the graph (pass false if you want to start the layout from the current position)
// 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
};
`
- 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.
* npm run test : Run Mocha tests in ./test
: Build ./src/* into cytoscape-cola.js
* : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)npm run dev
* : Automatically build on changes with live reloading with webpack dev servernpm run lint
* : Run eslint on the source
N.b. all builds use babel, so modern ES features can be used in the src.
This project is set up to automatically be published to npm and bower. To publish:
1. Build the extension : npm run build:release
1. Commit the build :
1. Bump the version number and tag:
1. Push to origin:
1. Publish to npm:
1. If publishing to bower for the first time, you'll need to run
1. Make a new release for Zenodo.