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,
  ...,
  log_transform = 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().
log_transform: A single logical value indicating whether to transform expression values using log(x + 1) before analysis. Default is TRUE. Set to FALSE for data that are already log-transformed.

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.

Details

By default, expression values are transformed using log(x + 1) before analysis. Set log_transform = FALSE to use the expression values as supplied, for example when they are already log-transformed.

Required packages