DIscBIO (version 1.2.2)

comptSNE: Computing tSNE

Description

This function is used to compute the t-Distributed Stochastic Neighbor Embedding (t-SNE).

Usage

comptSNE(
  object,
  rseed = NULL,
  max_iter = 5000,
  epoch = 500,
  quiet = FALSE,
  ...
)
# S4 method for DISCBIO
comptSNE(
  object,
  rseed = NULL,
  max_iter = 5000,
  epoch = 500,
  quiet = FALSE,
  ...
)

Value

The DISCBIO-class object input with the tsne slot filled.

Arguments

object

DISCBIO class object.

rseed

Random integer to to yield reproducible maps across different runs

max_iter

maximum number of iterations to perform.

epoch

The number of iterations in between update messages.

quiet

if `TRUE`, suppresses intermediate output

...

other parameters to be passed to `tsne::tsne`

Examples

sc <- DISCBIO(valuesG1msTest) # changes signature of data
sc <- Clustexp(sc, cln = 2) # data must be clustered before plottin
sc <- comptSNE(sc, max_iter = 30)
head(sc@tsne)