.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 1.12.0 Index]