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jbkinney / mavenn

MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect
MIT License
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Set global gauge #36

Open sofeasible opened 1 year ago

sofeasible commented 1 year ago

Is there a way to set the gauge for the whole experiment (such as early when defining the model) instead of within each visualization? I can't figure this out from the docs.

jbkinney commented 1 year ago

You can define an LxC probability matrix p_lc, then pass it to model.get_theta() using the user gauge by doing 

model.get_theta(gauge='user', p_lc=p_lc)

If you do this for every model that you fit, all the reported parameters will be in the same gauge defined by p_lc. See also: https://mavenn.readthedocs.io/en/latest/api.html#mavenn.Model.get_theta