How to make edges prominent?

[Former user]

Hello Sir, I am using Bio3D, and trying to generate communities network for my .dcd file. It is working fine but there is a slight issue, and I am unable to address it. The system generates a community file and after plotting I see all the communities overlapping each other. The problem is, that it actually hides the edges. Is there a way to make the edges prominent for a given generated community network? Cheers, Ash

[Xinqiu Yao]

Hi,

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You may adjust the layout and/or the size of communities to fix the issue. See help(plot.cna) and the vertex.size argument of the igraph.plotting()function from the igraph package.

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You can also add interactive=TRUE to the plotting function and adjust the layout interactively. Then, save the layout using, for example, layout <- tk_coords(1) where the number “1” should match the window number for the interactive community plot. Then, you can use the saved ‘layout’ for regularly plotting, for example plot(cna, layout=layout, ...)