runUMAP {CytoTree}R Documentation

Calculating UMAP

Description

Calculate Uniform Manifold Approximation and Projection in CYT

Usage

runUMAP(
  object,
  umap.config = umap.defaults,
  n_neighbors = 30,
  dims = 2,
  verbose = FALSE,
  ...
)

Arguments

object

an CYT object

umap.config

object of class umap.config. See umap.

n_neighbors

numeric. Number of neighbors

dims

numeric. Dim of umap, you can also change it in umap.config.

verbose

logical. Whether to print calculation progress.

...

Options to pass on to the umap function

Value

An CYT object

See Also

umap

Examples


cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- runUMAP(cyt, verbose = TRUE)
cyt <- runUMAP(cyt, n_neighbors = 20, verbose = TRUE)





[Package CytoTree version 1.4.0 Index]