densMAP implementation — rs_densmap_from

Leverages the densMAP implementation in manifolds-rs - a very fast Rust-based implementation. densMAP is UMAP with an added density-preserving term, so tight clusters stay tight and diffuse ones stay diffuse. This version uses a pre-computed kNN graph, please see new_nearest_neighbour().

Usage

rs_densmap_from_knn(
  embd,
  knn_data,
  n_dim,
  min_dist,
  spread,
  k,
  densmap_params,
  seed,
  use_high_precision,
  verbose
)

Arguments

embd: Numerical matrix. The data to use to generate the embeddings. Should be of dimensions samples x features.
knn_data: NearestNeighbours class from R.
n_dim: Integer. Number of densMAP dimensions to return.
min_dist: Numeric. Minimum distance to use.
spread: Numeric. Spread parameter to use.
k: Integer. Number of nearest neighbours to consider
densmap_params: Named list. List that contains all of the key parameters for the densMAP generation, i.e. the UMAP ones plus lambda, frac and var_shift.
seed: Integer. Seed for reproducibility.
use_high_precision: Optional logical. Controls fp32 vs fp64 for. If NULL will use sensible default thresholding.
verbose: Integer. If 0L -> silent or 1L for normal verbosity; 2L for detailed verbosity.

Value

The densMAP embeddings.

References

Narayan, Berger & Cho, Nature Biotechnology, 2021