generate_umap {FLAMES}R Documentation

Generate UMAP plot

Description

Generates the matrix of UMAP visualisation coordinates from a given SummarizedExperiment. The modified SummarizedExperiment object is returned, with UMAP coordinates stored in the 'reducedDims()' slot.

Usage

generate_umap(summarizedExperiment, counts = "counts")

Arguments

summarizedExperiment

the SingleCellExperiment of SummarizedExperiment object containing the counts to plot

counts

character string indicating the name of the assay to generate UMAP visualtization from. The assay should be accessable by 'assay(summarizedExperiemnt, counts)'.

Value

Modified SummarizedExperiment (or SingleCellExperiment) containing the UMAP visualisation coordinates in the 'reducedDims()' UMAP slot.

See Also

[sc_long_pipeline()]

[bulk_long_pipeline()]


[Package FLAMES version 0.99.31 Index]