Compute diffusion coordinates from a spectral basis — compute_diffusion

Diffusion coordinates at time $t$ are given by $\Phi \mathrm{diag}(\exp(-\lambda t))$, where $(\Phi,\lambda)$ are Laplacian eigenvectors/eigenvalues.

Usage

compute_diffusion_coordinates(
  basis = NULL,
  values = NULL,
  vectors = NULL,
  time = 1,
  k = NULL,
  eigen_tol = 1e-12,
  normalize = c("none", "row")
)

Arguments

basis: Optional basis list with fields `values` and `vectors`.
values: Optional numeric vector of eigenvalues (overrides `basis$values`).
vectors: Optional matrix (or sparse Matrix) of eigenvectors (overrides `basis$vectors`).
time: Positive numeric scalar or vector of times.
k: Optional integer number of coordinates to keep (defaults to all).
eigen_tol: Positive threshold; eigenpairs with `value <= eigen_tol` are dropped.
normalize: Optional normalization: `"none"` (default) or `"row"`.

Value

If `time` is length-1, a numeric matrix N x k. If `time` has length > 1, a list of matrices (one per time).