Run PHATE dimensionality reduction

Wrapper function into the Rust interface for PHATE. Constructs a kNN graph, computes alpha decay affinities, powers the diffusion operator to time t, and embeds via MDS on the resulting diffusion potential distances.

Usage

rs_phate(embd, n_dim, k, phate_params, seed, verbose)

Arguments

embd

Numerical matrix. The data to embed of shape samples x features.

n_dim

Integer. Number of PHATE dimensions to return. Currently only 2L is supported.

k

Integer. Number of nearest neighbours for graph construction.

phate_params

Named list. Contains all key parameters for PHATE, see params_phate() and params_nn().

seed

Integer. Seed for reproducibility.

verbose

Boolean. Controls verbosity of the function.

Value

The PHATE embedding as a matrix of shape samples x n_dim.