rtemis (version 0.79)

d.TSNE: t-distributed Stochastic Neighbor Embedding

Description

Perform t-SNE decomposition using Rtsne::Rtsne

Usage

d.TSNE(x, k = 3, initial.dims = 50, perplexity = 15, theta = 0,
  check.duplicates = TRUE, pca = TRUE, max.iter = 1000,
  scale = FALSE, center = FALSE, is.distance = FALSE,
  verbose = TRUE, outdir = "./")

Arguments

x

Input matrix

k

Integer. Number of t-SNE components required

initial.dims

Integer: Number of dimensions to retain in initial PCA. Default = 50

perplexity

Numeric: Perplexity parameter

theta

Float: 0.0: exact TSNE. Increase for higher speed, lower accuracy. Default = 0

check.duplicates

Logical: If TRUE, Checks whether duplicates are present. Best to set test manually

pca

Logical: If TRUE, perform initial PCA step. Default = TRUE

max.iter

Integer: Maximum number of iterations. Default = 1000

scale

Logical: If TRUE, scale before running t-SNE using base::scale. Default = FALSE

center

Logical: If TRUE, and scale = TRUE, also center. Default = FALSE

is.distance

Logical: If TRUE, x should be a distance matrix. Default = FALSE

verbose

Logical: If TRUE, print messages to output

outdir

Path to output directory

...

Options for Rtsne::Rtsne

Value

rtDecom object

See Also

Other Decomposition: d.CUR, d.H2OAE, d.H2OGLRM, d.ICA, d.ISOMAP, d.KPCA, d.LLE, d.MDS, d.NMF, d.PCA, d.SPCA, d.SVD, d.UMAP