Problems when generate community pictures

[xwind]

Hi, I am sorry I am not very familiar with the community analysis.

When I use the “plot(net, pdb)”, all the communities are overlapping. How to resolve the problem?

Meanwhile, how to color each community or change the label of the communities? Could you recommend any detailed tutorial (maybe step by step)?

Then which data in the “net“ object could generate the picture as attached before? I try “plot(neta$community.network,vertex.size=40,layout=layout.auto)”, but it shows larger than 14 communities. This is not the same as the picture I attached here (6 communities).

Thanks for your help.

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[Xinqiu Yao]

Many plotting parameters are inherited from the igraph package. For example, using ?igraph::igraph.plotting you can get the help documentation for some of your requests.

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Vertex sizes can be adjusted by vertex.size but you need to give a vector not just a single number. For example, vertex.size=V(net$community.network)$size*0.5

Above line will scale the size down to the half.

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The easy way to change color is probably changing the properties of network directly: V(net$community.netwokr)$color ←a vector of color names.

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Labels can be changed by the igraph parameter “vertex.label”. Check the help document for more detail.

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Here is a tutorial for network analysis:

http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

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Please take a look of the tutorial, try above suggestions, and then let me know if you still have problems.

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[xwind]

Thanks for your help. I get it.