Request: add methods to convert DAGs to networkx graphs

[AoifeHughes]

Hi,

I made a quick and dirty edit to allow for this: https://github.com/SirSharpest/goatools/commit/40be859be38f1d58978ebf454bf30006f7530840

For analysis and plotting of graphs networkx is often used, I beleive it would be useful for goatools to have the ability built in to export to and from networkx.

Perhaps this functionality is already possible, I was not able to find it in documentation.

Either way, I would be happy to integrate this properly and make a pull request if it would be of interest.

[tanghaibao]

@SirSharpest

Thank you. This will be a great contribution.

We do have some similar graph capabilities at this point. Would you mind taking a look at obo_parser.GODag.make_graph_pydot and .make_graph_pygraphviz, and see if you could add your method along with those?

Otherwise, please feel free to just create a pull request ... and we'll try to merge this in.

[tanghaibao]

@SirSharpest

Just noticed that your method is on GODagSmall so my previous suggestion (to modify GODag) doesn't apply. cc @dvklopfenstein to see what the best approach is here but it feels like we can extract your graph conversion as a method on GODagSmall.

[dvklopfenstein]

Hello @SirSharpest ,

Returning a networkx graph object containing significant GO terms is a great idea.

Rather than using the OboToGoDagSmall, which only accounts for connections up the is_a relationship, use GoSugDag, which will make it easier to expand in the future. It would look like this:

from goatools.gosubdag.gosubdag import GoSubDag
from goatools.gosubdag.go_edges import get_edgesobj

goids = [o.GO for o in goea_results if o.p_fdr_bh <= sig]
gosubdag = GoSubDag(goids, godag)
objedges = get_edgesobj(gosubdag)
edges = [(parent, child) for child, parent in objedges.edges]

The godag is a GODag object, which would need to be a new argument ot your function, GOs_to_nx.

To ensure a successful experience for people using your code, please:

• Write a test for your new code and include it in the pull request
• Run all your new code through pylint and ensure your code is rated 10.00/10
• Put the new code in the plotting directory: goatools/gosubdag/plot
• Ideally, you should run the full GOA Tools test suite before issuing the pull request

And if users have questions on your new code, you are willing to support it?

Thanks so much for the good idea and for the code.