network visualization (multiple data source integration)

Question

[lessismore]

Dear all,

i am dealing with network visualization and i would like to know if you feel like recommending tools for network visualization integrating multiple sources of data. For that i mean also including scores/colours/thickness features for edges based on multiple "evidences" on already computed networks. As far as i know, STRING with its R package or its App for Cytoscape provide a solid way to visualize it.

Here 2 questions:

1. some of you already used it? can you share your experience/give a user feedback?

2. Do you know better/valid alternatives?

thanks in advance for any help

Answer 1

[zizigolu]

Kevin has a tutorial here

Network plot from expression data in R using igraph

[Kevin Blighe]

Indeed. The 'framework' that I use in that tutorial is igraph, which is easy to use once you understand how its graph objects are constructed. Other published works, e.g., Phenograph, use igraph underneath the surface.

Answer 2

[manaswwm]

Of the tools that I have used so far:

-Gephi in my opinion has better layouts and visualization for large networks (compared to cytoscape) -GeneMania (available in cytoscape or as an independent tool on internet) has better visualization features for regular sized networks