Plotting large PPI biological networks

Question

[beingseema03]

Hi all,
I am analyzing HPRD dataset using R. I tried to plot my network using plot function in r. The problem is that i am not getting a better visualization of my biological network.It contains 9000 nodes and 39000 edges. Is there any way to better visualize the large PPI biological networks in R studio.

Answer 1

[raunakms]

I would suggest igraph R-package is very handy for graph analysis. You can export the graph files in different formats and import in interactive graph-visualization tools like Cytoscape

[beingseema03]

Hi @raunakms Thnks for reply.

Can you please provide some link or tutorial to refer..?? I tried Rcytoscape but my graph in unweighted and undirected so i failed to do it in rcytoscape. There are not any proper tutorials given for it.

Answer 2

[Sirus]

For big networks visualization, I think R is not the best choice, you can save it in R as gml format of a ncol format (if you don't have attributes in your nodes) and visualize it in some specialized tools such as Gephi.

Answer 3

[Joey]

If you want a high resolution graph with a bunch of options, cytoscape (http://www.cytoscape.org/) is a very good option to do the whole thing.

[beingseema03]

But i am facing one problem in cytoscape that my dataset is containing thousands of interaction and nodes. When i am plotting network in cytoscape the whole network is not visible in cytoscape and while zooming out the network the network will not remain in the understandable format.