Skip to contents

Run t-SNE on a SingleCells object (GPU)

tsne_gpu_sc.Rd

GPU-accelerated counterpart to bixverse::tsne_sc(). Runs tsne_gpu() on an embedding pulled from the object; only the kNN step is GPU-accelerated, the optimiser still runs on CPU (a GPU optimiser is on the roadmap).

t-SNE derives the number of neighbours from perplexity on the Rust side (the usual 3 * perplexity convention). To avoid a silent mismatch with the cached kNN, use_knn defaults to FALSE: every call generates a fresh GPU kNN sized to the requested perplexity. Handy for sweeping perplexities since the kNN is cheap on GPU.

Usage

tsne_gpu_sc(
  object,
  use_knn = FALSE,
  embd_to_use = "pca",
  slot_name = "tsne",
  no_embd_to_use = NULL,
  modality = c("rna", "adt", "wnn"),
  n_dim = 2L,
  perplexity = 20,
  approx_type = c("bh", "fft"),
  knn_method = c("nndescent", "exhaustive", "ivf"),
  nn_params = params_nn_gpu(),
  tsne_params = params_tsne_gpu(),
  seed = 42L,
  use_high_precision = NULL,
  .verbose = TRUE
)

Arguments

object

SingleCells (or SingleCellsMultiModal) class.

use_knn

Boolean. Defaults to FALSE. Set to TRUE to reuse the cached kNN; only sensible when the stored k is at least 3 * perplexity.

embd_to_use

String. The embedding to use for t-SNE. Must be available in the object for the chosen modality.

slot_name

String. The name of this embedding within the object. Defaults to "tsne".

no_embd_to_use

Optional integer. Number of embedding dimensions to use. If NULL, all will be used.

modality

String. On which modality to run t-SNE. One of c("rna", "adt", "wnn"). The two latter options are only available on SingleCellsMultiModal.

n_dim

Integer. Number of t-SNE dimensions. Currently only 2L is supported. Defaults to 2L.

perplexity

Numeric. Perplexity parameter. Typical values between 5 and 50. Defaults to 20.0.

approx_type

String. Approximation method. One of "bh" (Barnes-Hut) or "fft". Defaults to "bh". "fft" is Unix-only.

knn_method

String. GPU (approximate) nearest neighbour method. One of c("nndescent", "exhaustive", "ivf").

nn_params

Named list. GPU kNN parameters, see params_nn_gpu().

tsne_params

Named list. t-SNE (GPU) parameters, see params_tsne_gpu().

seed

Integer. For reproducibility.

use_high_precision

Optional boolean. Fine-grained fp32 vs fp64 control. GPU kNN is always fp32.

.verbose

Boolean or integer. Controls verbosity.

Value

The object with a "tsne" embedding added. If the requested embedding is missing, returns the object unchanged with a warning.

See also

tsne_gpu(), bixverse::tsne_sc(), umap_gpu_sc()