README.md

cytoscape-euler

Description

Euler is a fast, high-quality force-directed (physics simulation) layout for Cytoscape.js (demo)

It is based on cytoscape-ngraph.forcelayout, with several parts reworked and several general improvements.

Dependencies

• cytoscape@^3.0.0

Usage instructions

Download the library:

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

Import the library as appropriate for your project:

ES import:

import cytoscape from 'cytoscape';
import euler from 'cytoscape-euler';

cytoscape.use( euler );

CommonJS:

let cytoscape = require('cytoscape');
let euler = require('cytoscape-euler');

cytoscape.use( euler );

AMD:

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

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

API

Specify an options object with name: 'euler' to run the layout. All other fields are optional. An example with the default options follows:

let defaults = {
  name: 'euler',

  // The ideal length of a spring
  // - This acts as a hint for the edge length
  // - The edge length can be longer or shorter if the forces are set to extreme values
  springLength: edge => 80,

  // Hooke's law coefficient
  // - The value ranges on [0, 1]
  // - Lower values give looser springs
  // - Higher values give tighter springs
  springCoeff: edge => 0.0008,

  // The mass of the node in the physics simulation
  // - The mass affects the gravity node repulsion/attraction
  mass: node => 4,

  // Coulomb's law coefficient
  // - Makes the nodes repel each other for negative values
  // - Makes the nodes attract each other for positive values
  gravity: -1.2,

  // A force that pulls nodes towards the origin (0, 0)
  // Higher values keep the components less spread out
  pull: 0.001,

  // Theta coefficient from Barnes-Hut simulation
  // - Value ranges on [0, 1]
  // - Performance is better with smaller values
  // - Very small values may not create enough force to give a good result
  theta: 0.666,

  // Friction / drag coefficient to make the system stabilise over time
  dragCoeff: 0.02,

  // When the total of the squared position deltas is less than this value, the simulation ends
  movementThreshold: 1,

  // The amount of time passed per tick
  // - Larger values result in faster runtimes but might spread things out too far
  // - Smaller values produce more accurate results
  timeStep: 20,

  // The number of ticks per frame for animate:true
  // - A larger value reduces rendering cost but can be jerky
  // - A smaller value increases rendering cost but is smoother
  refresh: 10,

  // Whether to animate the layout
  // - true : Animate while the layout is running
  // - false : Just show the end result
  // - 'end' : Animate directly to the end result
  animate: true,

  // Animation duration used for animate:'end'
  animationDuration: undefined,

  // Easing for animate:'end'
  animationEasing: undefined,

  // Maximum iterations and time (in ms) before the layout will bail out
  // - A large value may allow for a better result
  // - A small value may make the layout end prematurely
  // - The layout may stop before this if it has settled
  maxIterations: 1000,
  maxSimulationTime: 4000,

  // Prevent the user grabbing nodes during the layout (usually with animate:true)
  ungrabifyWhileSimulating: false,

  // Whether to fit the viewport to the repositioned graph
  // true : Fits at end of layout for animate:false or animate:'end'; fits on each frame for animate:true
  fit: true,

  // Padding in rendered co-ordinates around the layout
  padding: 30,

  // Constrain layout bounds with one of
  // - { x1, y1, x2, y2 }
  // - { x1, y1, w, h }
  // - undefined / null : Unconstrained
  boundingBox: undefined,

  // Layout event callbacks; equivalent to `layout.one('layoutready', callback)` for example
  ready: function(){}, // on layoutready
  stop: function(){}, // on layoutstop

  // Whether to randomize the initial positions of the nodes
  // true : Use random positions within the bounding box
  // false : Use the current node positions as the initial positions
  randomize: false
};

cy.layout( defaults ).run();

Build instructions

• npm run build : Build ./src/** into cytoscape-euler.js
• npm run watch : 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 server
• npm 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:

1. Build the extension : npm run build:release
2. Commit the build : git commit -am "Build for release"
3. Bump the version number and tag: npm version major|minor|patch
4. Push to origin: git push && git push --tags
5. Publish to npm: npm publish .
6. If publishing to bower for the first time, you'll need to run bower register cytoscape-euler https://github.com/cytoscape/cytoscape.js-euler.git
7. Make a release on GitHub to automatically register a new Zenodo DOI