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CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement","maintainers":[{"email":"maxkfranz@gmail.com","name":"maxkfranz"},{"email":"dylanfong.ut@gmail.com","name":"dylanfong"},{"email":"mikekucera@gmail.com","name":"mikekucera"},{"email":"chrtannus@gmail.com","name":"chrtannus"},{"email":"shawn.reuland@gmail.com","name":"sreuland"},{"email":"jingjingbic@gmail.com","name":"ndexbio-org"},{"email":"metincansiper@gmail.com","name":"metincansiper"},{"email":"ugurdogrusoz@yahoo.com","name":"ugurdogrusoz"},{"email":"mj3cheun@gmail.com","name":"mj3cheun"},{"email":"balcihasan99@gmail.com","name":"balcihasan"}],"readme":"cytoscape-cose-bilkent\n================================================================================\n\n[![DOI](https://zenodo.org/badge/42200589.svg)](https://zenodo.org/badge/latestdoi/42200589)\n\n## Description\n\nThe CoSE (Compound Spring Embedder) layout for Cytoscape.js developed by [i-Vis Lab](http://cs.bilkent.edu.tr/~ivis/) in Bilkent University is a spring embedder layout with support for compound graphs (nested structures) and varying (non-uniform) node dimensions.\n([demo](https://raw.githack.com/cytoscape/cytoscape.js-cose-bilkent/master/demo.html), [compound demo](https://raw.githack.com/cytoscape/cytoscape.js-cose-bilkent/master/demo-compound.html))\n\nPlease cite the following when using this layout:\n\nU. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, \"[A Layout Algorithm For Undirected Compound Graphs](http://www.sciencedirect.com/science/article/pii/S0020025508004799)\", Information Sciences, 179, pp. 980-994, 2009.\n\n## Dependencies\n\n * Cytoscape.js ^3.2.0\n * cose-base ^1.0.0\n\n\n## Usage instructions\n\nDownload the library:\n * via npm: `npm install cytoscape-cose-bilkent`,\n * via bower: `bower install cytoscape-cose-bilkent`, or\n * via direct download in the repository (probably from a tag).\n\nImport the library as appropriate for your project:\n\nES import:\n\n```js\nimport cytoscape from 'cytoscape';\nimport coseBilkent from 'cytoscape-cose-bilkent';\n\ncytoscape.use( coseBilkent );\n```\n\nCommonJS require:\n\n```js\nlet cytoscape = require('cytoscape');\nlet coseBilkent = require('cytoscape-cose-bilkent');\n\ncytoscape.use( coseBilkent ); // register extension\n```\n\nAMD:\n\n```js\nrequire(['cytoscape', 'cytoscape-cose-bilkent'], function( cytoscape, coseBilkent ){\n  coseBilkent( cytoscape ); // register extension\n});\n```\n\nPlain HTML/JS has the extension registered for you automatically, because no `require()` is needed.\n\n\n## API\n\nWhen calling the layout, e.g. `cy.layout({ name: 'cose-bilkent', ... })`, the following options are supported:\n\n```js\nvar defaultOptions = {\n  // Called on `layoutready`\n  ready: function () {\n  },\n  // Called on `layoutstop`\n  stop: function () {\n  },\n  // 'draft', 'default' or 'proof\" \n  // - 'draft' fast cooling rate \n  // - 'default' moderate cooling rate \n  // - \"proof\" slow cooling rate\n  quality: 'default',\n  // Whether to include labels in node dimensions. Useful for avoiding label overlap\n  nodeDimensionsIncludeLabels: false,\n  // number of ticks per frame; higher is faster but more jerky\n  refresh: 30,\n  // Whether to fit the network view after when done\n  fit: true,\n  // Padding on fit\n  padding: 10,\n  // Whether to enable incremental mode\n  randomize: true,\n  // Node repulsion (non overlapping) multiplier\n  nodeRepulsion: 4500,\n  // Ideal (intra-graph) edge length\n  idealEdgeLength: 50,\n  // Divisor to compute edge forces\n  edgeElasticity: 0.45,\n  // Nesting factor (multiplier) to compute ideal edge length for inter-graph edges\n  nestingFactor: 0.1,\n  // Gravity force (constant)\n  gravity: 0.25,\n  // Maximum number of iterations to perform\n  numIter: 2500,\n  // Whether to tile disconnected nodes\n  tile: true,\n  // Type of layout animation. The option set is {'during', 'end', false}\n  animate: 'end',\n  // Duration for animate:end\n  animationDuration: 500,\n  // Amount of vertical space to put between degree zero nodes during tiling (can also be a function)\n  tilingPaddingVertical: 10,\n  // Amount of horizontal space to put between degree zero nodes during tiling (can also be a function)\n  tilingPaddingHorizontal: 10,\n  // Gravity range (constant) for compounds\n  gravityRangeCompound: 1.5,\n  // Gravity force (constant) for compounds\n  gravityCompound: 1.0,\n  // Gravity range (constant)\n  gravityRange: 3.8,\n  // Initial cooling factor for incremental layout\n  initialEnergyOnIncremental: 0.5\n};\n```\n\n*Note that this extension supports only relatively modern browsers.  Browsers like IE require significant shimming, for example with [core-js](https://www.npmjs.com/package/core-js).*\n\n*Note that while running Cytoscape.js in headless mode, stylingEnabled option of Cytoscape.js should be set as true because this extension considers node dimensions and some other styling properties.*\n\n\n## Build targets\n\n* `npm run test` : Run Mocha tests in `./test`\n* `npm run build` : Build `./src/**` into `cytoscape-cose-bilkent.js`\n* `npm run watch` : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)\n* `npm run dev` : Automatically build on changes with live reloading with webpack dev server\n* `npm run lint` : Run eslint on the source\n\nN.b. all builds use babel, so modern ES features can be used in the `src`.\n\n\n## Publishing instructions\n\nThis project is set up to automatically be published to npm and bower.  To publish:\n\n1. Build the extension : `npm run build:release`\n1. Commit the build : `git commit -am \"Build for release\"`\n1. Bump the version number and tag: `npm version major|minor|patch`\n1. Push to origin: `git push && git push --tags`\n1. Publish to npm: `npm publish .`\n1. If publishing to bower for the first time, you'll need to run `bower register cytoscape-cose-bilkent https://github.com/cytoscape/cytoscape.js-cose-bilkent.git`\n1. [Make a new release](https://github.com/cytoscape/cytoscape.js-cose-bilkent/releases/new) for Zenodo.\n","readmeFilename":"README.md"}