config.tsne.default: Default configuration for Rtsne

In KODAMA: Knowledge Discovery by Accuracy Maximization

Default configuration for Rtsne

Description

A list with parameters customizing a Rtsne embedding. Each component of the list is an effective argument for Rtsne_neighbors().

Usage

  config.tsne.default

Format

An object of class config.tsne.default of length 12.

Details

dims: integer, Output dimensionality

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

max_iter: integer, Number of iterations

verbose: logical, Whether progress updates should be printed (default: global "verbose" option, or FALSE if that is not set)

Y_init: matrix, Initial locations of the objects. If NULL, random initialization will be used (default: NULL). Note that when using this, the initial stage with exaggerated perplexity values and a larger momentum term will be skipped.

momentum: numeric, Momentum used in the first part of the optimization

final_momentum: numeric, Momentum used in the final part of the optimization

eta: numeric, Learning rate

exaggeration_factor:

num_threads: integer, Number of threads to use when using OpenMP, default is 1. Setting to 0 corresponds to detecting and using all available cores

define.n.cores: logical. If FALSE (default), KODAMA.visualization overrides num_threads using kk$n.cores from KODAMA.matrix output.

Examples

  # display all default settings
  config.tsne.default
  
  # create a new settings object with perplexity set to 100
  custom.settings = config.tsne.default
  custom.settings$perplexity = 100
  custom.settings
  

KODAMA documentation built on March 17, 2026, 5:07 p.m.