Cytoscape network viewer
================================

This tool takes gene interaction data from Intermine and visualises it using `cytoscape.js <http://js.cytoscape.org/>`_, a fabulous network visualisation tool. It replaces the flash-based CytoscapeWeb network viewer found in previous versions of the tool. 

Configuration
--------------------------

1. add the following entry to your '''webconfig-model.xml''' file:

.. code-block:: xml

	<reportdisplayer javaClass="org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer"
                jspName="model/cytoscapeNetworkDisplayer.jsp"
                replacesFields="interactions"
                placement="Interactions"
                types="Gene,Protein"/>
                

2. If you host your own `Intermine CDN <https://github.com/intermine/CDN>`_, make sure to pull the most recent update, as the interaction displayer script is loaded via CDN, under `js/intermine/gene-interaction-displayer`.

3. re-release your webapp and you should see the interaction displayer on gene report pages.

Data export format
---------------------------------------

The network visualisation can be exported as:

* PNG
* JPG
* TSV
* CSV

Implementation
------------------------------------------
This tool accesses the list of gene interactions for the target gene by calling a web service, sorting the data into edges and nodes, and inserting them into an HTML canvas for display. It can also be used externally to the report page as a stand alone application. For external setup instructions, see the `Cytoscape Intermine <https://github.com/yochannah/cytoscape-intermine>`_  repo, and the `standalone app demo page <http://yochannah.github.io/cytoscape-intermine/>`_

**Dependencies:** This tool uses `imjs <https://github.com/intermine/imjs>`_ to query the data, and `imtables <https://github.com/intermine/im-tables>`_ to display table data.

A short list of Java files found on the Intermine side:

CytoscapeNetworkDisplayer.java
	the report displayer class, get a set of genes interacting with the report gene, in your case, the genes/proteins on the same pathway as the report gene/protein

CytoscapeNetworkDisplayer.jsp
	the web page to display the network

CytoscapeNetworkService.java
	service class

.. index:: Cytoscape, SIF, XGMML, PNG, SVG, interactions, network viewer, interactions widget