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Wrapper function to generate diffusion maps parameters

params_diffusion_maps.Rd

Wrapper function to generate diffusion maps parameters

Usage

params_diffusion_maps(
  bandwidth_scale = 1,
  thresh = 1e-04,
  graph_symmetry = c("additive", "multiplicative", "mnn", "none"),
  alpha_norm = 1,
  t_max = 100L,
  t_custom = NULL,
  n_landmarks = 2048L,
  landmark_method = c("spectral", "random", "density"),
  n_svd = NULL
)

Arguments

bandwidth_scale

Numeric. Multiplicative factor applied to the adaptive kernel bandwidth. Defaults to 1.0.

thresh

Numeric. Sparsity threshold applied to kernel entries. Defaults to 1e-04.

graph_symmetry

String. Method used to symmetrise the affinity graph. One of c("additive", "multiplicative", "mnn", "none"). Defaults to "additive".

alpha_norm

Numeric. Anisotropic density-correction exponent. 0 gives the normalised graph Laplacian, 0.5 the Fokker-Planck operator, 1 the Laplace-Beltrami operator. Defaults to 1.0.

t_max

Integer. Maximum diffusion time considered during automatic selection via Von Neumann entropy knee point detection. Defaults to 100L.

t_custom

Integer or NULL. Fixed diffusion time. If set, overrides automatic time selection. Defaults to NULL.

n_landmarks

Integer or NULL. Number of landmarks for compressed diffusion. If NULL, the full N x N diffusion operator is used. Defaults to 2048L.

landmark_method

String. Method used to select landmarks. One of c("spectral", "random", "density"). Defaults to "spectral".

n_svd

Integer or NULL. Number of SVD components used in landmark construction. If NULL, the library selects a sensible default. Defaults to NULL.

Value

A named list with the following elements:

  • bandwidth_scale - Numeric. Multiplicative factor applied to the adaptive kernel bandwidth. Defaults to 1.0.

  • thresh - Numeric. Sparsity threshold applied to kernel entries. Defaults to 1e-04.

  • graph_symmetry - String. Method used to symmetrise the affinity graph. One of c("additive", "multiplicative", "mnn", "none"). Defaults to "additive".

  • alpha_norm - Numeric. Anisotropic density-correction exponent. 0 gives the normalised graph Laplacian, 0.5 the Fokker-Planck operator, 1 the Laplace-Beltrami operator. Defaults to 1.0.

  • t_max - Integer. Maximum diffusion time considered during automatic selection via Von Neumann entropy knee point detection. Defaults to 100L.

  • t_custom - Integer or NULL. Fixed diffusion time. If set, overrides automatic time selection. Defaults to NULL.

  • n_landmarks - Integer or NULL. Number of landmarks for compressed diffusion. If NULL, the full N x N diffusion operator is used. Defaults to 2048L.

  • landmark_method - String. Method used to select landmarks. One of c("spectral", "random", "density"). Defaults to "spectral".

  • n_svd - Integer or NULL. Number of SVD components used in landmark construction. If NULL, the library selects a sensible default. Defaults to NULL.