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cwatson / brainGraph

Graph theory analysis of brain MRI data
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Using brainGraph with ecological data. #7

Closed RGTake closed 5 years ago

RGTake commented 5 years ago

Hi Chris,

I am interested in using brainGraph package to access vertex roles in some igraph network I am working. My problem is I don't know what this {memb}{A numeric vector of membership indices of each vertex} means. Can I extract it from my igraph networks? Bear with me because I am a noobie at this. Thanks in advance.

Rodrigo

cwatson commented 5 years ago

I assume you are referring to gateway_coeff, part_coeff, or within_module_deg_z_score?

The memb variable can be anything you want, as long as the length of the vector equals the vertex count of your graph, and it only contains non-negative integers. It represents some partition of the vertices into different groups.

RGTake commented 5 years ago

Thanks Chris.

Yes, I refer to part_coeff, or within_module_deg_z_score.

Ok, so it must separate vertices into different groups. Does this groups enter the calculations? Because I can only think I can use species as a "group". My vertices represent different microbial species found in my samples. I could create a vector that would map to it but it would be very random.

Would it work?

cwatson commented 5 years ago

The typical/classic usage would be to use the output of a community detection algorithm for different groups. Specifically, the membership element of the algorithm's results. You can read the references specified in the functions' manual page for background information, and you can check out the code in set_brainGraph_attrs for how I call the functions you are asking about.

Let me know if you have other questions. Chris

cwatson commented 5 years ago

Hi @RGTake , I will close this issue; however, if I haven't sufficiently answered your questions you may re-open it.