[Nauty] help request

[Sean A. Irvine]

Hi Clément,

Others here with more experience will likely be able to help better, but
perhaps you can clarify a couple of points first.

Bicolored normally means that adjacent vertices do not have the same color,
how can you have that in the presence of loops?

What is the form of the output you are looking for?  Do you want the result
to be adjacency matrices like your example or something else?

Sean.




On Fri, 9 Apr 2021 at 05:14, clément galan <clement.galan at cri-paris.org>
wrote:

> Hello nauty users community,
>
> I'm a bioinformatics student in my first Master's year, currently doing an
> internship in a computational biology lab. My project is about generating
> an atlas of regulatory networks (i.e. graphs) on which we define ODE
> dynamics and then study their behaviour. To this end, we want to create
> 'all' graphs of a certain size. The graphs that we are considering are all
> the non isomorphic, directed and bicolored graphs with 4 vertices,
> including loops. Here is an example of the type of graph, as an adjacency
> matrix, that we aim to have (edges can take two values, 1 and -1):
> [image: image.png]
> After reading the documentation, I assumed that to use the nauty package
> was the most efficient way to generate all the graphs. However, I
> encountered some difficulties to correctly use the nauty / gtools
> functions, since my knowledge is still limited in this field. I would
> really appreciate if someone could give me indications to tackle my
> challenge.
>
> Best regards,
>
> Clément Galan
> CRI Paris and Inria Lyon
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