den-SNE implementation

Leverages the den-SNE implementation in manifolds-rs - a very fast Rust-based implementation. den-SNE is tSNE with an added density-preserving term, so tight clusters stay tight and diffuse ones stay diffuse. Setting lambda to 0 in the parameters recovers plain tSNE.

Usage

rs_densne(
  embd,
  n_dim,
  perplexity,
  approx_type,
  densne_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.

n_dim

Integer. Number of den-SNE dimensions to return. Needs to be two, others are not supported.

perplexity

Numeric. The tSNE perplexity parameter.

approx_type

String. One of c("fft", "bh"). Which of the two approximations to use.

densne_params

Named list. List that contains all of the key parameters for the den-SNE generation, i.e. the tSNE 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 den-SNE embeddings.

References

Narayan, Berger & Cho, Nature Biotechnology, 2021