Using MCC from TreeKnit

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

4 stars 1 forks source link

Closed nandsra21 closed 2 years ago

nandsra21 commented 2 years ago

Updating ha-na-nextstrain/2020-12-21NotebookFluHaNa.ipynb to use MCC from TreeKnit instead of clade_membership.
Would be good if clade_membership key used throughout the notebook could be a parameter at the top of the notebook.
Not every strain has an MCC value - the MCC should be calculated from only the rows in the dataframe where the TreeKnit MCC is defined

nandsra21 commented 2 years ago

nandsra21 commented 2 years ago

Fixed: Bullets 1 and 2. Working on: 3 and 4.