Run t-Stochastic Neighbour Embedding

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

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()