Overview

Compare Node Centralities with Cytoscape

This is an example of script to automatize Cytoscape. In this case, I have calculated different measures of node centralities in a network (thanks to the Centiscape plugin), and automatically generated a report to show the differences between them.

Pipeline:

  • create a network on Cytoscape
  • use the Centiscape plugin to calculate node centralities
  • install and activate the Cytoscape RPC plugin
  • Documentation for the Cytoscape RPC plugin and python: https://wiki.nbic.nl/index.php/CytoscapeRPC_Python_Example python scripts for Cytoscape
  • run the script
  • the plots will be generated in the figures/ directory
  • legends and histograms of distribution are generated with python's matplotlib (I couldn't find how to export the legend from RPC, and in any case, Cytoscape's legend looks ugly)