biojs-pcviz
BioJS component for PCViz embedded widget
About
PCViz is a web-based binary interaction visualizer that pulls in data from Pathway Commons. PCViz has an embedded widget option that can be used by other developers to easily show network on their web sites. This module wraps this functionality around BioJS framework for better and easier integration by developers.
Here some useful PCViz links:
- PCViz Homepage: http://www.pathwaycommons.org/pcviz
- PCViz on BioJS Registry: http://biojs.io/d/biojs-pcviz
- Pathway Commons: http://www.pathwaycommons.org/about/
Getting Started
Install the module with: npm install biojs-pcviz
or you can use the browser version from the latest build:
https://github.com/PathwayCommons/biojs-pcviz/tree/master/build
The following code sample shows how to use this component in a simple way:
var biojspcviz = ; // Create an instance of PCViz// and visualize the neighborhood of "BRCA1" gene in a div using this new instancevar yourDiv = document;var pcviz = el: yourDiv query: "BRCA1";pcviz;
You can find more examples under the examples
folder:
https://github.com/PathwayCommons/biojs-pcviz/tree/master/examples
Documentation
Default Options for Queries
var opts = // Target HTML element el: document // Base URL for the target PCViz instance baseurl: "http://sanderlab.org/pcviz/" // Width of the iframe width: "100%" // Height of the iframe height: "100%" // Query gene(s); delimited by comma (",") if more than one query: "MDM2" // If PCViz doesn't get loaded in this time, onFail will be called timeout: 20 * 1000 // Callback function for network load event {} // Callback function for node clicks; msg contains information about the node {} // Callback function for edge clicks; msg contains information about the edge {} // Callback function for background clicks; msg containts no information {} // Callback function to be called if network doesn't get loaded in timeout miliseconds. {}
.neighboorhood()
Visualizes the neighborhood of all query
genes.
Example:
// Loads neighborhood of BRCA2var pcviz = el: thatEl query: "BRCA2";pcviz;
.pathsbetween()
Queries the path between two or more genes.
Returns a less dense network compared to neighborhood
.
Example:
// Loads paths between TP53,MDM2var pcviz = el: thatEl query: "TP53,MDM2" ;pcviz;
Contributing
Please submit all issues and pull requests to the PathwayCommons/biojs-pcviz repository!
Support
If you have any problem or suggestion please open an issue here.
License
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this program. If not, see http://www.gnu.org/licenses/.