runUMAP: Calculating UMAP

Description Usage Arguments Value See Also Examples

View source: R/umap.R

Description

Calculate Uniform Manifold Approximation and Projection in CYT

Usage

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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

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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.