Improve clonotype network plot with plotAtlas

scverse / scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

https://scirpy.scverse.org/en/latest/

BSD 3-Clause "New" or "Revised" License

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Improve clonotype network plot with plotAtlas #318

Open grst opened 2 years ago

grst commented 2 years ago

Networkx now offers an "Atlas" example which could be useful for making nicer, packed plots that the current approach using "squarify". Not sure how it handles node sizes and probably the performance is not as good if there are many clonotypes, but it's definitely worth a look:

https://networkx.org/documentation/stable/auto_examples/graphviz_layout/plot_atlas.html#sphx-glr-auto-examples-graphviz-layout-plot-atlas-py

grst commented 10 months ago

Another alternative: https://github.com/paulbrodersen/netgraph