generate_umap {FLAMES} | R Documentation |
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.
generate_umap(summarizedExperiment, counts = "counts")
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)'. |
Modified SummarizedExperiment (or SingleCellExperiment) containing the UMAP visualisation coordinates in the 'reducedDims()' UMAP slot.
[sc_long_pipeline()]
[bulk_long_pipeline()]