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blab / cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
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Manually assign better seasonal flu clade colors #9

Closed huddlej closed 2 years ago

huddlej commented 3 years ago

The auto-assigned seasonal flu clade colors worked for a little while, but the latest iteration of the embeddings assigns colors that make related clades almost impossible to distinguish. Older clades that barely have any data get colors that should be used for larger extant clades.

For example, A2, A2/re, A3, and A4 are almost identically colored in the following figure:

image

We should go back to manually assigning colors to these clades, since there are a fixed number of clades in the analyses.

nandsra21 commented 3 years ago

Pushed a change to fix this. The old code has been made "raw" for now, but I can delete it completely if we decide these graphs look better.

huddlej commented 3 years ago

@nandsra21 Can you also use the same approach for 2018-2020 figure colors? Thank you!

nandsra21 commented 2 years ago

We can reopen if needed - but for right now we're only making HDBSCAN figures so "colors" is fine.