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leoisl / plasnet

Clustering, visualising and exploring plasmid networks
MIT License
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Second iteration hub plasmids not marked in visualisation #55

Open babayagaofficial opened 6 months ago

babayagaofficial commented 6 months ago

Hub plasmids get marked with a black star in the visualisation, and there's a toggle button that removes them, but any hub plasmids found in later iterations are black circles and don't get removed in the toggle. It also doesn't count them as present in the visualisation (even though they do get listed in hub_plasmids.csv).

iqbal-lab commented 5 months ago

@leoisl is this a hard or easy fix?

leoisl commented 5 months ago

Easy if you could send me an example where this happens. Then I can easily reproduce it and fix!

babayagaofficial commented 2 months ago

Hi @leoisl, I'm sorry I completely forgot about this issue and to send you an example. It happens in the Russian doll plasmids -- here's a screenshot of community 0: Screenshot from 2024-06-18 14-09-19

so pKPC_CAV1320 has been marked with a star as a hub, but the two black nodes beside it (pCAV1492-6393, pCAV1374-6538) have not. They are marked as hubs in hub_plasmids.csv though, and you can tell from the graph that they really are hubs. Looking at this example again, I'm actually not sure if the problem is that they're second iteration, or just that it's multiple hubs in one community.

I don't remember if you have any of the Russian doll data, so lmk if you need them sent to you.