runTsne: Run t-Stochastic Neighbour Embedding

In theMILOlab/SPATA2: A Toolbox for Spatial 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 = NULL, tsne_perplexity = 30, ...)

runTsne(...)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
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().
...	Additional arguments given to Rtsne::Rtsne().

Value

The updated input object, containing the added, removed or computed results.

See Also

runPCA(), getPcaDf(), getTsneDf(), getUmapDf()

Examples

library(SPATA2)

data("example_data")

object <- example_data$object_UKF269T_diet

object <- runPCA(object)
object <- runTSNE(object)
object <- runUMAP(object)

plotPCA(object, color_by = "histology")
plotTSNE(object, color_by = "histology")
plotUMAP(object, color_by = "histology")

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.