BioJS wrapper for PCViz widget from Pathway Commons team
npm install biojs-pcviz

> BioJS component for PCViz embedded widget
!PCViz Embedded Widget Screenshot
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/
npm install biojs-pcvizor 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
`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();
Please submit all issues and pull requests to the PathwayCommons/biojs-pcviz repository!
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/.