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cytoscape-cose-bilkent

The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement.

https://github.com/cytoscape/cytoscape.js-cose-bilkent

Science Score: 64.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: sciencedirect.com, zenodo.org
  • ✓
    Committers with academic emails
    3 of 12 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary

Keywords

cytoscapejs cytoscapejs-extension

Keywords from Contributors

graph-drawing network-visualization complexity-management diagramming network-analysis bioinformatics biology pathway-analysis sbgn systems-biology
Last synced: 6 months ago · JSON representation ·

Repository

The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement.

Basic Info
  • Host: GitHub
  • Owner: cytoscape
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Homepage:
  • Size: 16.9 MB
Statistics
  • Stars: 134
  • Watchers: 24
  • Forks: 46
  • Open Issues: 30
  • Releases: 12
Topics
cytoscapejs cytoscapejs-extension
Created over 10 years ago · Last pushed about 3 years ago
Metadata Files
Readme License Citation

README.md

cytoscape-cose-bilkent

DOI

Description

The CoSE (pron. "cosay", Compound Spring Embedder) layout for Cytoscape.js developed by i-Vis Lab in Bilkent University is a spring embedder layout with support for compound graphs (nested structures) and varying (non-uniform) node dimensions. A faster version of this layout style called fCoSE, also supporting user-defined placement constraints can be found here. (demo, compound demo)

Please cite the following when using this layout:

U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, 179, pp. 980-994, 2009.

Dependencies

  • Cytoscape.js ^3.2.0
  • cose-base ^1.0.0

Usage instructions

Download the library: * via npm: npm install cytoscape-cose-bilkent, * via bower: bower install cytoscape-cose-bilkent, 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 coseBilkent from 'cytoscape-cose-bilkent';

cytoscape.use( coseBilkent ); ```

CommonJS require:

```js let cytoscape = require('cytoscape'); let coseBilkent = require('cytoscape-cose-bilkent');

cytoscape.use( coseBilkent ); // register extension ```

AMD:

js require(['cytoscape', 'cytoscape-cose-bilkent'], function( cytoscape, coseBilkent ){ coseBilkent( cytoscape ); // register extension });

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

<script src="https://unpkg.com/layout-base/layout-base.js"></script> <script src="https://unpkg.com/cose-base/cose-base.js"></script> <script src="cytoscape-cose-bilkent.js"></script>

API

When calling the layout, e.g. cy.layout({ name: 'cose-bilkent', ... }), the following options are supported:

js var defaultOptions = { // Called on `layoutready` ready: function () { }, // Called on `layoutstop` stop: function () { }, // 'draft', 'default' or 'proof" // - 'draft' fast cooling rate // - 'default' moderate cooling rate // - "proof" slow cooling rate quality: 'default', // Whether to include labels in node dimensions. Useful for avoiding label overlap nodeDimensionsIncludeLabels: false, // number of ticks per frame; higher is faster but more jerky refresh: 30, // Whether to fit the network view after when done fit: true, // Padding on fit padding: 10, // Whether to enable incremental mode randomize: true, // Node repulsion (non overlapping) multiplier nodeRepulsion: 4500, // Ideal (intra-graph) edge length idealEdgeLength: 50, // Divisor to compute edge forces edgeElasticity: 0.45, // Nesting factor (multiplier) to compute ideal edge length for inter-graph edges nestingFactor: 0.1, // Gravity force (constant) gravity: 0.25, // Maximum number of iterations to perform numIter: 2500, // Whether to tile disconnected nodes tile: true, // Type of layout animation. The option set is {'during', 'end', false} animate: 'end', // Duration for animate:end animationDuration: 500, // Amount of vertical space to put between degree zero nodes during tiling (can also be a function) tilingPaddingVertical: 10, // Amount of horizontal space to put between degree zero nodes during tiling (can also be a function) tilingPaddingHorizontal: 10, // Gravity range (constant) for compounds gravityRangeCompound: 1.5, // Gravity force (constant) for compounds gravityCompound: 1.0, // Gravity range (constant) gravityRange: 3.8, // Initial cooling factor for incremental layout initialEnergyOnIncremental: 0.5 };

Note that this extension supports only relatively modern browsers. Browsers like IE require significant shimming, for example with core-js.

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.

Build targets

  • npm run test : Run Mocha tests in ./test
  • npm run build : Build ./src/** into cytoscape-cose-bilkent.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-cose-bilkent https://github.com/cytoscape/cytoscape.js-cose-bilkent.git
  7. Make a new release for Zenodo.

Owner

  • Name: Cytoscape Consortium
  • Login: cytoscape
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Dogrusoz"
  given-names: "Ugur"
  orcid: "https://orcid.org/0000-0002-7153-0784"
- family-names: "Giral"
  given-names: "Erhan"
- family-names: "Cetintas"
  given-names: "Ahmet"
- family-names: "Civril"
  given-names: "Ali" 
- family-names: "Demir"
  given-names: "Emek"    
title: "cytoscape-cose-bilkent"
version: 4.1.0
date-released: 2019-09-09
url: "https://github.com/cytoscape/cytoscape.js-cose-bilkent"
preferred-citation:
  type: article
  authors:
  - family-names: "Dogrusoz"
    given-names: "Ugur"
    orcid: "https://orcid.org/0000-0002-7153-0784"
  - family-names: "Giral"
    given-names: "Erhan"
  - family-names: "Cetintas"
    given-names: "Ahmet"
  - family-names: "Civril"
    given-names: "Ali" 
  - family-names: "Demir"
    given-names: "Emek"
  doi: "10.1016/j.ins.2008.11.017"
  journal: "Information Sciences"
  month: 3
  start: 980 # First page number
  end: 994 # Last page number
  title: "A layout algorithm for undirected compound graphs"
  issue: 7
  volume: 179
  year: 2009

GitHub Events

Total
  • Issues event: 1
  • Watch event: 6
  • Issue comment event: 1
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 6
  • Issue comment event: 1
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 232
  • Total Committers: 12
  • Avg Commits per committer: 19.333
  • Development Distribution Score (DDS): 0.612
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
hasanbalci b****9@g****m 90
metincansiper m****r@g****m 64
Max Franz m****z@g****m 48
Dylan Fong d****g@u****a 7
Manfred Cheung m****n@u****a 7
ugurdogrusoz u****z@g****m 4
Sebastian Tilsch s****h@i****e 4
Alexander Li a****0@g****m 3
JLHwung i@j****e 2
Josejulio Martínez f****z@g****m 1
kinimesi i****i@s****r 1
dorukcakmakci d****7@g****m 1
Committer Domains (Top 20 + Academic)
uwaterloo.ca: 2 std.sehir.edu.tr: 1 jhuang.me: 1 itaricon.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 50
  • Total pull requests: 51
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 32
  • Total pull request authors: 10
  • Average comments per issue: 3.34
  • Average comments per pull request: 1.22
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 25
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ugurdogrusoz (11)
  • maxkfranz (6)
  • finger563 (2)
  • d2fong (2)
  • Does666 (2)
  • mikpom (1)
  • MistyKuu (1)
  • glampr (1)
  • umdstu (1)
  • galaxym51 (1)
  • hasanbalci (1)
  • metincansiper (1)
  • heyjohnnyfunt (1)
  • zhpeh (1)
  • mr-loop-1 (1)
Pull Request Authors
  • dependabot[bot] (24)
  • maxkfranz (9)
  • hasanbalci (7)
  • metincansiper (3)
  • josejulio (2)
  • bradh (1)
  • mmartinmo (1)
  • d2fong (1)
  • JLHwung (1)
  • adhusson (1)
Top Labels
Issue Labels
enhancement (12) bug (3) invalid (1)
Pull Request Labels
dependencies (24) enhancement (1)

Packages

  • Total packages: 3
  • Total downloads:
    • npm 5,737,506 last-month
  • Total docker downloads: 1,686,698,355
  • Total dependent packages: 54
    (may contain duplicates)
  • Total dependent repositories: 10,361
    (may contain duplicates)
  • Total versions: 113
  • Total maintainers: 9
npmjs.org: cytoscape-cose-bilkent

The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement

  • Versions: 53
  • Dependent Packages: 48
  • Dependent Repositories: 10,337
  • Downloads: 5,737,506 Last month
  • Docker Downloads: 1,686,698,320
Rankings
Downloads: 0.2%
Dependent repos count: 0.2%
Docker downloads count: 0.6%
Dependent packages count: 0.6%
Average: 1.8%
Forks count: 4.1%
Stargazers count: 4.7%
Maintainers (9)
chrtannus mikekucera cytoscapenpm maxkfranz dylanfong metincansiper balcihasan mj3cheun ugurdogrusoz
Last synced: 6 months ago
bower.io: cytoscape-cose-bilkent

The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement

  • License: MIT
  • Latest release: v4.1.0
    published over 6 years ago
  • Versions: 55
  • Dependent Packages: 1
  • Dependent Repositories: 4
Rankings
Dependent packages count: 3.1%
Average: 7.7%
Forks count: 8.1%
Dependent repos count: 9.7%
Stargazers count: 9.8%
Last synced: 6 months ago
repo1.maven.org: org.webjars.npm:cytoscape-cose-bilkent

WebJar for cytoscape-cose-bilkent

  • Versions: 5
  • Dependent Packages: 5
  • Dependent Repositories: 20
  • Docker Downloads: 35
Rankings
Dependent repos count: 5.4%
Dependent packages count: 11.5%
Average: 16.8%
Forks count: 24.3%
Stargazers count: 26.2%
Last synced: 6 months ago

Dependencies

bower.json bower
  • cose-base ^1.0.0
  • cytoscape ^3.2.0
package-lock.json npm
  • 1097 dependencies
package.json npm
  • babel-core ^6.24.1 development
  • babel-loader ^7.0.0 development
  • babel-preset-env ^1.5.1 development
  • camelcase ^4.1.0 development
  • chai 4.0.2 development
  • cpy-cli ^1.0.1 development
  • cross-env ^5.0.0 development
  • eslint ^3.9.1 development
  • gh-pages ^1.0.0 development
  • mocha 3.4.2 development
  • npm-run-all ^4.1.2 development
  • rimraf ^2.6.2 development
  • update ^0.7.4 development
  • updater-license ^1.0.0 development
  • webpack ^2.6.1 development
  • webpack-dev-server ^2.4.5 development
  • cose-base ^1.0.0