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 1.0.2 Index]