runTSNE: Perform t-SNE dimensionality reduction

In rliger: Linked Inference of Genomic Experimental Relationships

Perform t-SNE dimensionality reduction

Description

Runs t-SNE on the aligned cell factors (result from alignFactors), or unaligned cell factors (result from runIntegration)) to generate a 2D embedding for visualization. By default Rtsne (Barnes-Hut implementation of t-SNE) method is invoked, while alternative "fftRtsne" method (FFT-accelerated Interpolation-based t-SNE, using Kluger Lab implementation) is also supported. For very large datasets, it is recommended to use method = "fftRtsne" due to its efficiency and scalability.

Extra external installation steps are required for using "fftRtsne" method. Please consult detailed guide.

Usage

runTSNE(
  object,
  useRaw = NULL,
  useDims = NULL,
  nDims = 2,
  usePCA = FALSE,
  perplexity = 30,
  theta = 0.5,
  method = c("Rtsne", "fftRtsne"),
  dimredName = "TSNE",
  asDefault = NULL,
  fitsnePath = NULL,
  seed = 42,
  verbose = getOption("ligerVerbose", TRUE),
  k = nDims,
  use.raw = useRaw,
  dims.use = useDims,
  use.pca = usePCA,
  fitsne.path = fitsnePath,
  rand.seed = seed
)

Arguments

object	liger object with factorization results.
useRaw	Whether to use un-aligned cell factor loadings (H matrices). Default NULL search for aligned factor loadings first and un-aligned loadings then.
useDims	Index of factors to use for computing the embedding. Default NULL uses all factors.
nDims	Number of dimensions to reduce to. Default 2.
usePCA	Whether to perform initial PCA step for Rtsne. Default FALSE.
perplexity	Numeric parameter to pass to Rtsne (expected number of neighbors). Default 30.
theta	Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE. Default 0.5.
method	Choose from "Rtsne" or "fftRtsne". See Description. Default "Rtsne".
dimredName	Name of the variable in cellMeta slot to store the result matrix. Default "TSNE".
asDefault	Logical, whether to set the resulting dimRed as default for visualization. Default NULL will set it when no default is set.
fitsnePath	Path to the cloned FIt-SNE directory (i.e. '/path/to/dir/FIt-SNE'). Required only when first time using runTSNE with method = "fftRtsne". Default NULL.
seed	Random seed for reproducibility. Default 42.
verbose	Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
use.raw, dims.use, k, use.pca, fitsne.path, rand.seed	Deprecated. See Usage section for replacement.

Value

The object where a "TSNE" variable is updated in the cellMeta slot with the whole 2D embedding matrix.

See Also

runUMAP

Examples

pbmc <- runTSNE(pbmcPlot)

rliger documentation built on Aug. 27, 2025, 1:08 a.m.