Refactor clonotype_imbalance

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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Refactor clonotype_imbalance #160

Open grst opened 4 years ago

grst commented 4 years ago

Analogous to #156, at some point

[ ] make volcano and dotplot a different function
[ ] make clear what is computed by the tool and what on-the-fly
[ ] more compact representation for dotplot, potentially a heatmap could work.
[ ] speed up:
- use implementation of fisher's test that approximates using chi-square when sample size is large enough
- should be trivial to parallelize

grst commented 3 years ago

Potentially, clonotype_imbalance will be made obsolte by clonotype_modularity. For now, I marked clonotype_imbalance as deprecated with a note asking the user to switch to clonotype modularity, or drop an issue if that doesn't fit their use-case.

Let's see how that goes, in the meanwhile, clonotype_imbalance will remain as is.