Wrapper function for the BBKNN parameters

Wrapper function for the BBKNN parameters

Usage

params_sc_bbknn(
  neighbours_within_batch = 3L,
  set_op_mix_ratio = 1,
  local_connectivity = 1,
  trim = NULL,
  knn = list()
)

Arguments

neighbours_within_batch

Integer. Number of neighbours to consider per batch. Defaults to 3L.

set_op_mix_ratio

Numeric. Mixing ratio between union (1.0) and intersection (0.0). Defaults to 1.0.

local_connectivity

Numeric. UMAP connectivity computation parameter, how many nearest neighbours of each cell are assumed to be fully connected. Defaults to 1.0.

trim

Optional integer. Trim the neighbours of each cell to these many top connectivities. May help with population independence and improve the tidiness of clustering. If NULL, it defaults to 10 * neighbours_within_batch.

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 BBKNN parameters.