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Uniform Manifold Approximation and Projection (UMAP)

gly_umap.Rd

Perform UMAP dimensionality reduction on the expression data. The function uses uwot::umap() to perform UMAP analysis.

Usage

gly_umap(exp, n_neighbors = 15, n_components = 2, add_info = TRUE, ...)

Arguments

exp

A glyexp::GlycomicSE() or glyexp::GlycoproteomicSE() object, or another SummarizedExperiment containing an expression matrix and sample information.

n_neighbors

Number of neighbors to consider for each point. Default is 15.

n_components

Number of output dimensions. Default is 2.

add_info

A logical value. If TRUE (default), sample information from the experiment will be added to the result tibble. If FALSE, only the UMAP coordinates are returned.

...

Additional arguments passed to uwot::umap().

Value

A list with three elements:

  • tidy_result: A tibble with UMAP coordinates containing the following columns:

    • sample: Sample name

    • umap1: First UMAP dimension

    • umap2: Second UMAP dimension

    • umap3, umap4, etc.: Additional UMAP dimensions (if n_components > 2)

  • raw_result: The raw UMAP result matrix

  • meta_data: A list containing metadata from the input experiment The list has classes glystats_umap_res and glystats_res.

Required packages

This function requires the uwot package to be installed for UMAP analysis.

See also

uwot::umap()