Biallelic pairwise distances and neighbour joining trees

malariagen / malariagen-data-python

Analyse MalariaGEN data from Python

https://malariagen.github.io/malariagen-data-python/latest/

MIT License

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Biallelic pairwise distances and neighbour joining trees #470

Closed alimanfoo closed 8 months ago

alimanfoo commented 8 months ago

Adds a new function plot_njt() for plotting neighbour-joining trees.
Adds a supporting function biallelic_diplotype_pairwise_distances() for computing a distance matrix.
Refactors plot_haplotype_clustering(), plot_pca_coords() and plot_pca_coords_3d() to use common code for setting up plotting colors and symbols where possible.
Some maintenance to docs and poetry.
Small optimisation to add memory caching within snp_calls().
Expose tqdm_class parameter to allow overriding what type of tqdm output is used for progress.

njt2

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alimanfoo commented 8 months ago

Building on proof of concept here.

codecov[bot] commented 8 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (ab5c0a1) 98.06% compared to head (ab54891) 98.08%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #470 +/- ## ========================================== + Coverage 98.06% 98.08% +0.02% ========================================== Files 26 28 +2 Lines 2174 2198 +24 ========================================== + Hits 2132 2156 +24 Misses 42 42 ```

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alimanfoo commented 8 months ago

Going to merge soon here as the njt feature is needed for an analysis project, but there's a lot going on in this PR so very happy to revisit anything here.