runTsne: Run t-Stochastic Neighbour Embedding

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Run t-Stochastic Neighbour Embedding

Description

Takes the pca-data of the object up to the principal component denoted in argument n_pcs and performs tSNE with it.

Usage

runTsne(object, n_pcs = 20, tsne_perplexity = 30, of_sample = NA, ...)

runTsne2(object, n_pcs = 20, tsne_perplexity = 30, of_sample = NA, ...)

Arguments

object	A valid spata-object.
n_pcs	Numeric value. Denotes the number of principal components used. Must be smaller or equal to the number of principal components the pca data.frame contains.
tsne_perplexity	Numeric value. Given to argument perplexity of Rtsne::Rtsne().
of_sample	This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.
...	Additional arguments given to Rtsne::Rtsne().

Value

• runTsne(): An updated spata-object containing the reduction variables in the tsne data.frame.

• runTsne2(): The direct output-object of Rtsne::Rtsne()

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.