cytoscape-symmap
v4.0.0
Published
The Symmap physics simulation layout for Cytoscape.js
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cytoscape-spread
Description
The Spread physics simulation layout for Cytoscape.js (demo) (proteins demo)
The spread layout uses a force-directed physics simulation with several external libraries. The layout tries to keep elements spread out evenly, making good use of constrained space.
The layout makes use of CoSE (MIT) and rhill-voronoi-core.js
(MIT). CoSE is already bundled in Cytoscape.js, and rhill-voronoi-core.js
is bundled in cytoscape-spread
.
There are two phases to this layout:
(1) A force-directed layout provides initial positions for the nodes. By default, the embedded version of CoSE is used, because it is fast and because it does not increase your app's bundle size any more than using Cytoscape.js itself. You can use an alternative layout by specifying options.prelayout
with the layout options you want to use for the first phase (e.g. { name: 'grid' }
). Alternatively, you can specify options.prelayout: false
(falsey) to just use the node's existing positions for the first phase.
(2) Voronoi is used to spread out the nodes in the remaining space.
Note that since you are composing layouts with phase (1), where options.prelayout
is non-falsey, you will have more layout events. For example, you will have more than one layoutstop
event -- one for the Spread layout overall and one for the prelayout within phase (1) of Spread.
If you skip phase (1) with options.prelayout
falsey, you will not get extra events within Spread. You can use promise chaining with two layouts to get the same effect as running a layout in phase (1), i.e.:
var layout1 = cy.makeLayout({ name: 'cose' });
var layout2 = cy.makeLayout({ name: 'spread', prelayout: false });
var run = function(l){
var p = l.promiseOn('layoutstop');
l.run();
return p;
};
(
Promise.resolve()
.then(function(){ return run(layout1); })
.then(function(){ return run(layout2); })
.then(function(){ console.log('done 1 and 2') })
);
Dependencies
- Cytoscape.js ^3.0.0
- Weaver.js ^1.2.0
Usage instructions
Download the library:
- via npm:
npm install cytoscape-spread
, - via bower:
bower install cytoscape-spread
, 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 spread = require('cytoscape-spread');
spread( cytoscape ); // register extension
AMD:
require(['cytoscape', 'cytoscape-spread', 'weaverjs'], function( cytoscape, spread, weaver ){
spread( cytoscape, weaver ); // register extension
});
Plain HTML/JS has the extension registered for you automatically, because no require()
is needed. However, the weaverjs library must be included as well.
API
Call the layout, e.g. cy.layout({ name: 'spread', ... })
, with options:
var defaults = {
animate: true, // Whether to show the layout as it's running
ready: undefined, // Callback on layoutready
stop: undefined, // Callback on layoutstop
fit: true, // Reset viewport to fit default simulationBounds
minDist: 20, // Minimum distance between nodes
padding: 20, // Padding
expandingFactor: -1.0, // If the network does not satisfy the minDist
// criterium then it expands the network of this amount
// If it is set to -1.0 the amount of expansion is automatically
// calculated based on the minDist, the aspect ratio and the
// number of nodes
prelayout: { name: 'cose' }, // Layout options for the first phase
maxExpandIterations: 4, // Maximum number of expanding iterations
boundingBox: undefined, // Constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
randomize: false // Uses random initial node positions on true
};
Build targets
npm run test
: Run Mocha tests in./test
npm run build
: Build./src/**
intocytoscape-spread.js
npm run watch
: Automatically rebuild on source changesnpm run lint
: Run eslint on the source
N.b. all builds use babel, so modern ES features can be used in the src
.
Publishing instructions
This project is set up to automatically be published to npm and bower. To publish:
- Build the extension :
npm run build:release
- Commit the build :
git commit -am "Build for release"
- Bump the version number and tag:
npm version major|minor|patch
- Push to origin:
git push && git push --tags
- Publish to npm:
npm publish .
- If publishing to bower for the first time, you'll need to run
bower register cytoscape-spread https://github.com/cytoscape/cytoscape.js-spread.git
- Make a new release for Zenodo.