TODO: optimize distance calculations at different tax levels

jsevo / taxumap

MIT License

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TODO: optimize distance calculations at different tax levels #20

Open jsevo opened 2 years ago

jsevo commented 2 years ago

When using cityblock, we won't have to do what's happening here:

https://github.com/jsevo/taxumap/blob/61165d1f879fee4bab359597bcd63f494dd7b6ce/taxumap/tools.py#L20

The distances can be calculated at ASV level and then the columns of distance matrices can be added based on taxonomy. This distance works, maybe others too.

jsevo commented 2 years ago

Another optimization that is easily possible: allow the user to provide a pre-calculated distance; overall distance or per taxonomic level.