dimred_tsne {dyndimred}

tSNE

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)