.bhtsne {CellTrails}R Documentation

#' DEF: Truncate eigenbasis #' #' For details see reduceDimensions #' @keywords internal #' @author Daniel C. Ellwanger .reduceDimensions_def <- function(x, s) CellTrails::latentSpace(x) <- CellTrails::latentSpace(x)[, seq_len(s@n)] CellTrails::eigenvalues(x) <- CellTrails::eigenvalues(x)[seq_len(s@n)] x t-Distributed Stochastic Neighbor Embedding

Description

Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

Usage

.bhtsne(x, dims = 2, perplexity = 30, theta = 0.5, max_iter = 1000)

Arguments

x

A numerical matrix

dims

Output dimensionality

perplexity

Perplexity parameter (default: 30)

theta

Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact tSNE (default: .5)

max_iter

Number of iterations (default: 1000)

Value

A list with the following components:

Y

Matrix containing the new representations for the objects

perplexity

See above

Author(s)

Daniel C. Ellwanger


[Package CellTrails version 1.10.0 Index]