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t-SNE embedding

Source: R/embeddings.R
cuda_tsne.Rd

t-SNE currently uses the CPU Rtsne backend.

Usage

cuda_tsne(
  x,
  n_components = 2L,
  perplexity = 30,
  theta = 0.5,
  seed = NULL,
  ...,
  reduced_dim = NULL
)

Arguments

x

Numeric observation-by-feature matrix, compatible cudaverse result, or a SingleCellExperiment with a reduced dimension.

n_components

Output dimensions.

perplexity

t-SNE perplexity.

theta

Barnes-Hut accuracy/speed trade-off.

seed

Optional random seed.

...

Additional arguments passed to Rtsne::Rtsne().

reduced_dim

For a SingleCellExperiment, the reduced-dimension name to embed. When NULL, a compatible recorded metadata choice is used first, followed by a uniquely named "PCA". Other names must be selected explicitly.

Value

A cuda_embedding; see cuda_umap() for the stable result fields.

Examples

if (requireNamespace("Rtsne", quietly = TRUE)) {
  cuda_tsne(matrix(rnorm(120), 40, 3), perplexity = 5, seed = 1)
}
#> <cuda_embedding method=tsne observations=40 dimensions=2 backend=Rtsne compute_device=cpu>