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Wrapper function to generate densMAP parameters

params_densmap.Rd

The density-preservation knobs on top of the usual UMAP parameters. densMAP adds -lambda * Corr(log Ro, log Re) to the UMAP loss, where Ro is the local radius in the input space and Re the matching radius in the embedding. Setting lambda to 0 recovers plain UMAP.

Usage

params_densmap(lambda = 2, frac = 0.3, var_shift = 0.1)

Arguments

lambda

Numeric. Weight of the density term. 0 disables it. The default is the densMAP reference value. Defaults to 2.0.

frac

Numeric. Fraction of the total epochs, at the end of the run, over which the density term is active. Defaults to 0.3.

var_shift

Numeric. Additive shift on the variance of the embedding log-radii. Defaults to 0.1.

Value

A named list with the following elements:

  • lambda - Numeric. Weight of the density term. 0 disables it. The default is the densMAP reference value. Defaults to 2.0.

  • frac - Numeric. Fraction of the total epochs, at the end of the run, over which the density term is active. Defaults to 0.3.

  • var_shift - Numeric. Additive shift on the variance of the embedding log-radii. Defaults to 0.1.

References

Narayan, Berger & Cho, Nat. Biotechnol., 2021