# biojs-pcviz

[![NPM version](http://img.shields.io/npm/v/biojs-pcviz.svg)](https://www.npmjs.org/package/biojs-pcviz)
[![Build Status](https://secure.travis-ci.org/PathwayCommons/biojs-pcviz.png?branch=master)](http://travis-ci.org/PathwayCommons/biojs-pcviz)

> BioJS component for PCViz embedded widget

## About
[PCViz](http://www.pathwaycommons.org/pcviz/) is a web-based binary interaction visualizer that pulls in data from [Pathway Commons](http://www.pathwaycommons.org/about).
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.

![PCViz Embedded Widget Screenshot](pcviz-screenshot.png)

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:

```javascript
var biojspcviz = require('biojs-pcviz');

// Create an instance of PCViz
// and visualize the neighborhood of "BRCA1" gene in a div using this new instance
var yourDiv = document.getElementById('yourDiv');
var pcviz = new biojspcviz({ el: yourDiv, query: "BRCA1"});
pcviz.neighborhood();
```

You can find more examples under the `examples` folder:

https://github.com/PathwayCommons/biojs-pcviz/tree/master/examples

## Documentation

### Default Options for Queries

```javascript
var opts = {
  // Target HTML element
  el: document.createElement("div"),
  // 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
  onLoad: function(msg) {},
  // Callback function for node clicks; msg contains information about the node
  onNodeClick: function(msg) {},
  // Callback function for edge clicks; msg contains information about the edge
  onEdgeClick: function(msg) {},
  // Callback function for background clicks; msg containts no information
  onBackgroundClick: function(msg) {},
  // Callback function to be called if network doesn't get loaded in timeout miliseconds.
  onFail: function() {}
}
```

#### .neighboorhood()
Visualizes the neighborhood of all `query` genes.

Example:
```javascript
// Loads neighborhood of BRCA2
var pcviz = new biojspcviz({ el: thatEl, query: "BRCA2"});
pcviz.neighborhood();
```

#### .pathsbetween()
Queries the path between two or more genes.
Returns a less dense network compared to `neighborhood`.

Example:
```javascript
// Loads paths between TP53,MDM2
var pcviz = new biojspcviz({ el: thatEl, query: "TP53,MDM2" });
pcviz.pathsbetween();
```

## Contributing

Please submit all issues and pull requests to the [PathwayCommons/biojs-pcviz](http://github.com/PathwayCommons/biojs-pcviz) repository!

## Support
If you have any problem or suggestion please open an issue [here](https://github.com/PathwayCommons/biojs-pcviz/issues).

## 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/.