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Refactor clonotype_imbalance

Open grst opened this issue 5 years ago • 1 comments

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 avatar Jun 04 '20 15:06 grst

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.

grst avatar Aug 24 '21 13:08 grst