runUMAP: Calculating UMAP

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

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	a 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

A 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)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.