runUMAP: Perform dimension reduction through UMAP

In casanova-lab/iMUBAC: Integration of Multi-Batch Cytometry datasets

Perform dimension reduction through UMAP

Description

runUMAP takes an SCE object and computes UMAP coordinates using uwot.

Usage

runUMAP(
  sce,
  by_exprs_values = "exprs",
  name = "UMAP",
  n_components = 2,
  n_neighbors = 100,
  min_dist = 0.5,
  scale = T,
  n_threads = parallel::detectCores(logical = F),
  seed = 12345
)

Arguments

sce	A SingleCellExperiment object.
by_exprs_values	A character string. Specifies which assay data to use for clustering.
name	A character string. Specifies the name of the reduced dimensions.
n_components, n_neighbors, min_dist, scale, n_threads	See umap.
seed	Numeric. Sets a random seed.

Value

A SingleCellExperiment-class object.

casanova-lab/iMUBAC documentation built on Sept. 13, 2022, 6:36 p.m.