biojs-vis-psicquic v1.1.3

biojs-vis-PSICQUICGraph

About

PSICQUICGraph is a BioJS component to visualize molecular interactions from PSICQUIC services. Click here to see a working example!

Getting Started

Install it using npm: npm install biojs-vis-psicquic

    var yourDiv = document.getElementById('snippetDiv');
    //Require the app
    var biojsvispsicquic = require('biojs-vis-psicquic');
    
    // Intercept elements before rendering in order to set property type based on intTypes
        var intercept = function(elements){
            for (i = 0, len = elements.edges.length; i < len; i++) { 
                elements.edges[i].data.type = elements.edges[i].data.intTypes[0].value;
            }
            return elements;
        };

        // Create container div
        var yourDiv = document.getElementById('snippetDiv');
            yourDiv.style.left = 0;
            yourDiv.style.top = 0;
            yourDiv.style.width = "100%";
            yourDiv.style.height = "100%";
            yourDiv.style.position = "absolute";

        var cyopts = {
            container:yourDiv,
            ready: function(){ 
                console.log('rendering finished.') 
            },
            headless: false,
            renderer: {
                name: 'canvas'
            },
          style: cytoscape.stylesheet()
            .selector('node')
              .css({
                'height': 80,
                'width': 80,
                'content': 'data(id)',
                'text-valign': 'center',
                'color': 'white',
                'border-color': '#000',
                'border-width': 3,
                'border-opacity': 0.5
              })
            .selector('edge')
              .css({
                'curve-style': 'haystack',
                'opacity': 0.6,
                'width': 'mapData(normalized_max_weight, 0, 0.01, 5, 10)'
              })
            .selector('edge[type = "association"]')
                .css({
                    'line-color': '#D0B7D3'
                })
            .selector('edge[type = "physical association"]')
                .css({
                    'line-color': '#9BD8DD'
                })
            .selector('edge[type = "direct interaction"]')
                .css({
                    'line-color': '#A0B3D8'
                })
            .selector('edge[type = "atpase reaction"]')
                .css({
                    'line-color': '#EAA2A3'
                })
        ,
        layout: {
            name: 'concentric',
            concentric: function(){
                return this.data('weight');
            },
            levelWidth: function(nodes){
                return 0.5;
            },
            padding: 10
          }
        };
        
        // IntAct REST url
        var url = 'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search';
        
        // User heroku proxy
        var proxy = function(url){
            return 'https://cors-anywhere.herokuapp.com/'+url;
        };
        
        //Init the app
        biojsvispsicquic.url(url)
            .query('species:human&id:(BRCA1 OR BRCA2)')
            .proxy(proxy)
            .cyopts(cyopts)
            .intercept(intercept)
            .update();

Cite

If you use PSICQUICGraph please cite the article here.

Contributing

Please submit all issues and pull requests to the jmVillaveces/biojs-vis-psicquic repository!

Support

If you have any problem or suggestion please open an issue here.

License

This software is licensed under the Apache 2 license, quoted below.

Copyright (c) 2014, José Villaveces

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.