runUMAP: runUMAP

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Wrapper for the umap function.

Usage

runUMAP(object, ..., method, config)

## S4 method for signature 'EMSet'
runUMAP(object, ..., method = c("naive", "umap-learn"),
  config = NULL)

Arguments

object	An EMSet
...	Additional arguments to pass to the UMAP function
method	Method to use with the UMAP function - naive (default) or umap-learn (Python package required)
config	Configuration to use with UMAP function (Optional)

Value

UMAP matrix stored in "UMAP" slot in reducedDims

Examples

# Load example EMSet
em_set <- ascend::analyzed_set

# Run UMAP
em_set <- runUMAP(em_set, method = "naive")

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.