Rust-based PHATE — phate • manifoldsR

Performs PHATE dimensionality reduction on the input data. This function provides a user-friendly interface with input validation before calling the Rust implementation.

Usage

phate(
  data,
  knn = NULL,
  n_dim = 2L,
  k = 5L,
  knn_method = c("balltree", "hnsw", "annoy", "nndescent", "exhaustive"),
  nn_params = params_nn(),
  phate_params = params_phate(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

data: Numerical matrix or data frame. The data to embed of shape samples x features. Will be coerced to a matrix.
knn: Optional NearestNeighbours class. If provided, PHATE will skip the k-nearest neighbour graph generation and use this one instead. The k argument must match the k used to generate this graph. Defaults to NULL.
n_dim: Integer. Number of dimensions in the embedding space. Currently only 2L is supported. Defaults to 2L.
k: Integer. Number of nearest neighbours for graph construction. Defaults to 5L.
knn_method: Character. Approximate nearest neighbour algorithm to use. One of "hnsw", "annoy", "nndescent", "balltree", or "exhaustive". Defaults to "balltree".
nn_params: Named list. Nearest neighbour search parameters, see params_nn().
phate_params: Named list. PHATE algorithm parameters, see params_phate().
seed: Integer. Random seed for reproducibility. Defaults to 42L.
.verbose: Logical. Controls verbosity. Defaults to TRUE.

Value

A numerical matrix with dimensions samples x n_dim containing the PHATE embedding.