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Run t-SNE dimensionality reduction.

Source: R/Visualization.r
CalculateTSNE.Rd

The function CalculateTSNE is used to run t-SNE dimensionality reduction.

Usage

CalculateTSNE(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)

# S3 method for iSCMEBObj
CalculateTSNE(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)

# S3 method for iSCMEBResObj
CalculateTSNE(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)

# S3 method for list
CalculateTSNE(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)

Arguments

obj

A iSCMEBObj object or a iSCMEBResObj object or a list of low dimension embeddings.

reduction

The name of embeddings to be used to calculate t-SNE. If reduction is null, the last added one is used for plotting.

n_comp

An optional positive integer, specify the number of features to be extracted.

seed

A random seed to be used.

toList

An indicator of whether convert the UMAP representation to a list.

Value

Returns a revised iSCMEBObj object.

Returns a revised iSCMEBResObj object.

Returns the UMAP matrix.

See also

iSCMEBObj-class, fit.iscmeb, iSCMEBResObj-class

Examples

data(iSCMEBObj_toy)
#> Warning: data set 'iSCMEBObj_toy' not found
library(Seurat)
iSCMEBObj_toy <- CalculateTSNE(iSCMEBObj_toy, reduction="iSCMEB")
## resList <- CalculateTSNE(iSCMEBObj_toy@resList, reduction="iSCMEB")