Uniform Manifold Approximation and Projection (UMAP)

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, ...)

gly_umap_(expr_mat, n_neighbors = 15, n_components = 2, ...)

Arguments

exp: A glyexp::experiment() object containing 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. Only applicable to gly_umap().
...: Additional arguments passed to uwot::umap().
expr_mat: A numeric matrix with variables as rows and samples as columns.

Value

A list with two 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 The list has classes glystats_umap_res and glystats_res.

Details

gly_umap() is the top-level API that works with glyexp::experiment() objects and supports the add_info parameter for joining experiment metadata.

gly_umap_() is the underlying API that works with matrices directly, providing more flexibility for users who don't use the glyexp package.

Required packages