Question: network visualization (multiple data source integration)
1
gravatar for lessismore
6 months ago by
lessismore690
Mexico
lessismore690 wrote:

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

ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 6 months ago by lessismore690
3
gravatar for Angel
6 months ago by
Angel3.5k
Angel3.5k wrote:

Kevin has a tutorial here

Network plot from expression data in R using igraph

ADD COMMENTlink written 6 months ago by Angel3.5k

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.

ADD REPLYlink written 6 months ago by Kevin Blighe48k
3
gravatar for manaswwm
6 months ago by
manaswwm30
manaswwm30 wrote:

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

ADD COMMENTlink written 6 months ago by manaswwm30
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