Wrapper function for the SEACells parameters

Usage

params_sc_seacells(
  n_sea_cells,
  max_fw_iters = 50L,
  convergence_epsilon = 0.001,
  max_iter = 100L,
  min_iter = 10L,
  greedy_threshold = 20000L,
  graph_building = "union",
  pruning = FALSE,
  pruning_threshold = 1e-07,
  knn = list()
)

Arguments

n_sea_cells: Integer. Number of SEA cells to detect.
max_fw_iters: Integer. Maximum iterations for the Franke-Wolfe algorithm. Defaults to 50L.
convergence_epsilon: Numeric. Convergence threshold. Algorithm stops when RSS change < epsilon * RSS(0). Defaults to 1e-3.
max_iter: Integer. Maximum iterations to run SEACells for. Defaults to 100L.
min_iter: Integer. Minimum iterations to run SEACells for. Defaults to 10L.
greedy_threshold: Integer. Maximum number of cells before defaulting to rapid random selection of archetypes. Defaults to 20000L.
graph_building: String. Graph building method. Defaults to "union".
pruning: Boolean. Shall tiny values be pruned during Franke-Wolfe updates. This will reduce memory pressure and can be a good option on large data sets. Defaults to FALSE.
pruning_threshold: Float. If pruning = TRUE values below which threshold shall be pruned.
knn: List. Optional overrides for kNN parameters. See params_knn_defaults() for available parameters: k, knn_method, ann_dist, search_budget, n_trees, delta, diversify_prob, ef_budget, m, ef_construction, ef_search, n_list and n_probe.

Value

A list with the SEACells parameters.