• 9/1/2015: Version 0.5.0 release. View utilities added.
• 6/27/2014: Version 0.4.3 release. Minor update version for Python 3.4.x.
• 6/26/2014: Version 0.4.2 release. Confirmed to work with cyREST 1.1.0.
• 6/23/2014: Version 0.4.1 release. Graph utility modules have been updated.
• 6/4/2014: Version 0.4.0 release. This is still in alpha.

py2cytoscape is a collection of utilities to use Cytoscape and Cytoscape.js from Python. Network visualization feature is still limited in Python, but with this tool, you can access both of Cytoscape and Cytoscape.js as network visualization engines for your Python code!

This package is still experimental and in alpha status.

Cytoscape is a de-facto standard desktop application for network visualization in bioinformatics community. But actually, it is a domain-independent graph visualization software for all typs of network data analysis. We want to introduce cy2cytoscape, along with cyREST and Jupyter Notebook, to broader data science community.

We recommend that you install most of the py2cytoscape dependent packages with Miniconda Python package manager.

~/miniconda2/bin/conda install scipy pandas networkx jupyter
~/miniconda2/bin/pip install py2cytoscape

conda install scipy pandas networkx jupyter

Next download python-igraph whl file from http://www.lfd.uci.edu/~gohlke/pythonlibs/ and

pip install THE_PYTHON_IGRAPH.whl

Finally,

pip install py2cytoscape

cyREST is a language-agnostic RESTful API for Cytoscape 3. Of course you can drive Cytoscape by calling raw RESTful API using requests or other http client library, but with this wrapper, you can significantly reduce your lines of code.

# HTTP Client for Python
import requests

# Standard JSON library
import json

# Basic Setup
PORT_NUMBER = 1234
BASE = 'http://localhost:' + str(PORT_NUMBER) + '/v1/'

# Header for posting data to the server as JSON
HEADERS = {'Content-Type': 'application/json'}

# Define dictionary of empty network
empty_network = {
        'data': {
            'name': 'I\'m empty!'
        },
        'elements': {
            'nodes':[],
            'edges':[]
        }
}

res = requests.post(BASE + 'networks?collection=My%20Collection', data=json.dumps(empty_network), headers=HEADERS)
new_network_id = res.json()['networkSUID']
print('Empty network created: SUID = ' + str(new_network_id))

from py2cytoscape.data.cyrest_client import CyRestClient

cy = CyRestClient()
network = cy.network.create(name='My Network', collection='My network collection')
print(network.get_id())

You can use Cytoscape.js network visualization widget in Jupyter Notebook. This is particulaly useful when you share your network analysis results with others.

Cytoscape.js JSON is one of the standard data exchange formats in Cytoscape community. py2cytoscape includes some graph data conversion utilities for popular graph analysis packages in Python.

Currently, the following graph objects are supported:

• NetworkX - From / To Cytoscape.js JSON
• igraph - From / To Cytoscape.js JSON
• pandas DataFrame - To Cytoscape.js JSON

And these popular libraries will be supported soon:

• Numpy adj. matrix (binary/weighted)
• graph-tool
• GraphX
• GraphLab