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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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Create an MCC_by_mds_parameters graph #14

Closed nandsra21 closed 2 years ago

nandsra21 commented 3 years ago

make the graph/picture with n_components in the x axis and validation_mcc in the y. Fix in summarize-grid-search, and the respective workflows (seasonal-flu, zika, mers, sars)

nandsra21 commented 2 years ago

Looks like this issue is bigger than expected - after removing the hardcoded value for n_components from cluster_by_parameters, all the integer values in the config file are being cast to float at some point during this parsing. This is making it impossible to run MDS, as n_components must be an int. Trying to resolve issue now.

nandsra21 commented 2 years ago

Adding n_components to "TYPE_BY_PARAMETER": TYPE_BY_PARAMETER = { "n_neighbors": int, "n_components": int } fixed that problem. I'm going to check the final tsv file when its done to make sure it looks right, and then I'll add this graph. It may turn out that more than 2 components should be used.

nandsra21 commented 2 years ago

I'll add the other grid searches once they finish! closing for now.