cytoscape-sbgn-stylesheet

A Cytoscape.js package that provides SBGN specific glyph styles (demo)

Purpose

To render SBGN-PD(Systems Biology Graphical Notation) graphs -- a visual language for representing biological processes.

Installation

Install via npm

npm install cytoscape-sbgn-stylesheet

Usage

Initialize cytoscape.js and call this module as a stylesheet parameter

var cytoscape = require('cytoscape');
var sbgnStylesheet = require('cytoscape-sbgn-stylesheet');

var cy = cytoscape({
  container: container,
  style: sbgnStylesheet(cytoscape),
  // other arguments here
});

Requirements

Input needs to be formatted Cytoscape.js graph JSON.

The following graph JSON structure is required:

{
  nodes: [],  // array of nodes
  edges: []   // array of edges
}

Supported SBGN PD glyphs

simple chemical multimer
macromolecule multimer
nucleic acid feature multimer
complex multimer
simple chemical
macromolecule
nucleic acid feature
compartment
unspecified entity
perturbing agent
complex
phenotype
tag
process
uncertain process
omitted process
source and sink
dissociation
association
and
or
not

Supported SBGN PD arcs

necessary stimulation
production
consumption
stimulation
catalysis
inhibition

Unsupported SBGN PD glyphs

submap
ports

The following node JSON structure is required:

      "data": {
        "id": "glyph23",                   // id of the node
        "class": "simple chemical",        // class of the node (see classes section for a list of supported sbgn glyphs
        "label": "Ca2+",                   // label to be displayed on the node
        "parent": "glyph2",                // parent node id if any
        "clonemarker": false,              // whether the node has a clonemarker or not
        "stateVariables": [],              // an array of state variables
        "unitsOfInformation": [],          // an array of units of information
      }

The following edge JSON structure is required:

      "data": {
        "id": "glyph19-glyph5",            // id
        "class": "production",             // sbgn class
        "cardinality": 0,                  // cardinality
        "source": "glyph19",               // source node id
        "target": "glyph5",                // target node id
        "portSource": "glyph19",           // port of the source
        "portTarget": "glyph5"             // port of the target
      }

To get Cytoscape.js graph JSON, you need the following:

SBGN-ML files; xml files that represent biological networks.
An SBGN-ML to Cytoscape.js converter.

Style Incompatibilities

The following cytoscape.js style properties are used to render SBGN PD graphics. Overriding these entirely will produce unexpected behaviour:

shape
width
height
background-image
background-width
background-position-x
background-position-y
background-fit
background-clip
padding
border-width

Run targets

npm run build : build project
npm run build-prod : build the project for production
npm run bundle-profile : visualise the bundle dependencies
npm run clean : clean the project
npm run watch : watch mode (debug mode enabled, autorebuild, autoreload)
npm test : run tests
npm run lint : lint the project

Testing

All files /test will be run by Mocha. You can npm test to run all tests, or you can run mocha -g specific-test-name (prerequisite: npm install -g mocha) to run specific tests.

Chai is included to make the tests easier to read and write.

Publishing a release

Make sure the tests are passing: npm test
Do a prod build: npm run build-prod
Make sure the linting is passing: npm run lint
Bump the version number with npm version, in accordance with semver. The version command in npm updates both package.json and git tags, but note that it uses a v prefix on the tags (e.g. v1.2.3).
For a bug fix / patch release, run npm version patch.
For a new feature release, run npm version minor.
For a breaking API change, run npm version major.
For a specific version number (e.g. 1.2.3), run npm version 1.2.3.
Push the release: git push origin --tags
Publish to npm: npm publish .

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