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scMetaTraj (version 0.1.1)

scMetaTraj_embed: Embed cells in metabolic feature space

Description

scMetaTraj_embed() constructs a low-dimensional representation of cells based on pathway-level metabolic scores.

DESIGN PRINCIPLES:

  • PCA is the true analysis space (for graph construction).

  • UMAP is ONLY for visualization.

Usage

scMetaTraj_embed(
  scores,
  method = c("PCA", "UMAP"),
  n_pcs = 10,
  umap_n_neighbors = 30,
  umap_min_dist = 0.3,
  seed = 123
)

Value

A numeric matrix:

  • PCA: cells x PCs

  • UMAP: cells x 2

Arguments

scores

Numeric matrix, cells x pathways.

method

Character. "PCA" (default) or "UMAP".

n_pcs

Integer. Number of PCs to return / use.

umap_n_neighbors

Integer. UMAP n_neighbors.

umap_min_dist

Numeric. UMAP min_dist.

seed

Integer. Random seed.