plot graph with dot

[kexul]

Hi, I've seen your discussion here michellab/BioSimSpace#193 , @JenkeScheen said:

if you've done any work on LOMAP network generation to show within a notebook that would be very helpful! It's starting to look like the LOMAP build I currently have is unable to draw a decent-looking network to show in an ipynb.

The network drawn by pygraphviz has several drawbacks:
1. The edge would be covered by molecule image.
2. The molecule image would cover each other when there are many molecule pairs.
I would recommend use dot to generate network graph as LOMAP have done, which doesn't have the drawbacks listed above.
I've copied some code from my project and created a gist to show how to do that with several lines:
https://gist.github.com/kexul/044340c773822c7748c722b9e2e082e2

Core lines:

1. Add image file and label, here labelloc='t' means label is at top of node.

G.add_node(name, image=fname, label = name, labelloc='t')

2. Generate .dot file and convert it to .png.

nx.nx_agraph.write_dot(G, f'temp/{file_name}.dot')
os.system(f'dot -Tpng temp/{file_name}.dot -o temp/{file_name}.png')

[lohedges]

Thanks, @kexul. This is very helpful. I agree that the network plot quickly becomes a mess as the number of ligand pairs grow. This seems like a great approach and will be easy to implement.

[JenkeScheen]

Ah! LOMAP generates a dot plot too, there should be a file in the work-dir, that could save us some work. I remember looking at the saved image during early dev and not liking it, but I think that must have been because we were only generating partial graphs at that point. Thanks for the suggestion @kexul! Get Outlook for Android<https://aka.ms/ghei36>

…

________________________________ From: Lester Hedges ***@***.***> Sent: Saturday, April 24, 2021 10:51:43 AM To: michellab/bss_fep_advanced_tut_bg ***@***.***> Cc: SCHEEN Jenke ***@***.***>; Mention ***@***.***> Subject: Re: [michellab/bss_fep_advanced_tut_bg] plot graph with dot (#1) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe. Thanks, @kexul<https://github.com/kexul>. This is very helpful. I agree that the network plot quickly becomes a mess as the number of ligand pairs grow. This seems like a great approach and will be easy to implement. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKJEIKI5IQSK64Q5FLIALMTTKKIC7ANCNFSM43P5OV3Q>. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.