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Plotting large PPI biological networks

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.

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updated by Ram Ram • written by beingseema03 • beingseema03

3 answers

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

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written by raunakms raunakms

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.

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written by beingseema03 • beingseema03

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.

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written by Sirus Sirus

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.

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updated by Ram Ram • written by Joey Joey

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.

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written by beingseema03 • beingseema03

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