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Wrapper function to generate PHATE parameters

params_phate.Rd

Wrapper function to generate PHATE parameters

Usage

params_phate(
  decay = 40,
  bandwidth_scale = NULL,
  t_max = 100L,
  t_custom = NULL,
  gamma = 1,
  n_landmarks = 2048L,
  landmark_method = c("spectral", "random", "density"),
  n_svd = NULL,
  mds_method = c("sgd_dense", "classic"),
  graph_symmetry = c("additive", "multiplicative", "mnn", "none")
)

Arguments

decay

Numeric. Alpha decay parameter controlling the kernel bandwidth. Higher values create sharper transitions. Defaults to 40.0.

bandwidth_scale

Numeric or NULL. Scaling factor applied to the kernel bandwidth. If NULL, the library selects a sensible default. Defaults to NULL.

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.

gamma

Numeric. Informational distance parameter for the diffusion potential. Defaults to 1.0.

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.

mds_method

String. MDS algorithm used for the final embedding. One of c("sgd_dense", "classic"). Defaults to "sgd_dense".

graph_symmetry

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

Value

A named list with the following elements:

  • decay - Numeric. Alpha decay parameter controlling the kernel bandwidth. Higher values create sharper transitions. Defaults to 40.0.

  • bandwidth_scale - Numeric or NULL. Scaling factor applied to the kernel bandwidth. If NULL, the library selects a sensible default. Defaults to NULL.

  • 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.

  • gamma - Numeric. Informational distance parameter for the diffusion potential. Defaults to 1.0.

  • 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.

  • mds_method - String. MDS algorithm used for the final embedding. One of c("sgd_dense", "classic"). Defaults to "sgd_dense".

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