Inter-community couplings

[Former user]

Dear Bio3d developer: I printed the inter-community couplings using $community.cij for my network of interest, which yields the same values of E(net$community.network)$weight, but in a more human readable fashion. I noticed, however, that the edges between communities having smaller weights were thicker than those with higher weight values when representing the communities as interconnected circles. I want to know the reason for this, and I would appreciate a lot a brief explanation on how inter-community couplings are calculated. Thanks a lot, Jorge

[Xinqiu Yao]

Hi,

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By default, network edges (both residue wise and community wise) are weighted by -log(|cij|), which means if two nodes have a strong correlation the weight will be small (i.e., the weight represents "distance" between nodes). However, in the plot, we want to highlight highly correlated communities, and thereby the edge width is proportional to |cij|. By default, the inter-community correlation is calculated by the maximal |cij| between all nodes of the two communities. It can be changed by the collapse.method argument of the cna() function.

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