RaceID (version 0.1.3)

comptsne: Computation of a two dimensional t-SNE representation

Description

This functions performs the computation of a t-SNE map from the distance object in slot distances using the Rtsne package.

Usage

comptsne(object, initial_cmd = TRUE, perplexity = 30, rseed = 15555)

Arguments

object

SCseq class object.

initial_cmd

logical. If TRUE, then the t-SNE map computation is initialized with a configuration obtained by classical multidimensional scaling. Default is TRUE.

perplexity

Positive number. Perplexity of the t-SNE map. Default is 30.

rseed

Integer number. Random seed to enforce reproducible t-SNE map.

Value

SCseq object with t-SNE coordinates stored in slot tsne.

Examples

# NOT RUN {
sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- comptsne(sc)
# }