Meaning and function of the n_components parameter

[Marius1311]

Harmony has a n_components parameter, which, according to the docstring:

:param pc_components: Minimum number of principal components to use. Specify `None` to use pre-computed components

That value is used for utils.run_pca, but it's not passed over to scanpy's neighboor computation, see

Harmony/src/harmony/core.py

Line 67 in eca0771

sc.pp.neighbors(temp, n_pcs=0, n_neighbors=n_neighbors)

So I wonder what the significance of that parameter actually is?

Also, I find the default value of 1000 a bit high, as scanpy's default here is much smaller, 50 I believe

[ManuSetty]

The n_components parameter is used below

Harmony/src/harmony/core.py

Line 48 in eca0771

pca_projections, _ = utils.run_pca(data_df, n_components=pc_components)

to compute the principal components.

In line 67, temp is already pre-computed principal components and thus the parameter is not passed for nearest neighbor computation.