Run Uniform Manifold Approximation and Projection — runUMAP • SPATA2

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

runUMAP(object, n_pcs = NULL, ...)

runUmap(...)

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.
...: Additional arguments given to umap::umap().

Value

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

See also

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")