Wrapper function to generate PHATE parameters

Usage

params_phate(
  decay = 40,
  bandwidth_scale = NULL,
  t_max = 100L,
  t_custom = NULL,
  gamma = 1,
  n_landmarks = 2024L,
  landmark_method = "spectral",
  n_svd = NULL,
  mds_method = "sgd_dense",
  graph_symmetry = "additive"
)

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. When 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. When 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. When NULL, the full N x N diffusion operator is used. Defaults to 2048L.
landmark_method: Character. Method used to select landmarks. One of "spectral", "random", or "density". Defaults to "spectral".
n_svd: Integer or NULL. Number of SVD components used in landmark construction. When NULL, the library selects a sensible default. Defaults to NULL.
mds_method: Character. MDS algorithm used for the final embedding. One of "sgd_dense" or "classic". Defaults to "sgd_dense".
graph_symmetry: Character. Method used to symmetrise the affinity graph. One of "additive", "multiplicative", "mnn", or "none". Defaults to "additive".

Value

A list with the PHATE parameters.