dimred_tsne: tSNE

In dyndimred: Dimensionality Reduction Methods in a Common Format

Description

tSNE

Usage

dimred_tsne(
  x,
  ndim = 2,
  perplexity = 30,
  theta = 0.5,
  initial_dims = 50,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

Arguments

x	Log transformed expression data, with rows as cells and columns as features
ndim	The number of dimensions
perplexity	numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)
theta	numeric; Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE (default: 0.5)
initial_dims	integer; the number of dimensions that should be retained in the initial PCA step (default: 50)
distance_method	The name of the distance metric, see dynutils::calculate_distance

See Also

Rtsne::Rtsne()

Examples

library(Matrix)
dataset <- abs(Matrix::rsparsematrix(100, 100, .5))
dimred_tsne(dataset, ndim = 3)

dyndimred documentation built on March 23, 2021, 9:06 a.m.