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dpeerlab / Harmony

Harmony framework for connecting scRNA-seq data from discrete time points
GNU General Public License v2.0
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Scanpy Implementation does not expose n_neighbors #11

Closed Marius1311 closed 4 years ago

Marius1311 commented 4 years ago

The scanpy implementation computes the augmented affinity matrix via

 # compute the augmented and non-augmented affinity matrices
    aug_aff, aff = harmony.core.augmented_affinity_matrix(
        adata.to_df(), adata.obs[tp], timepoint_connections, pc_components=n_components,
    )

Unfortunately, it does not expose the n_neighbors parameter, which would be quite important to be able to choose.

awnimo commented 4 years ago

Hey @Marius1311 Thank for pointing this out, we will update the implementation and have all parameters for the function exposed.

Marius1311 commented 4 years ago

Thanks @awnimo !

ManuSetty commented 4 years ago

Fixed in 6e34c6aa64753226656d90b663be362a08467f6a