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Wrapper function for the BBKNN parameters

params_sc_bbknn.Rd

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

Integer or NULL. 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. Defaults to NULL.

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, extract_knn, m, ef_construction, ef_search, n_list and n_probe. See params_knn_defaults() for the available elements. Defaults to list().

Value

A named list with the following elements:

  • 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 - Integer or NULL. 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. Defaults to NULL.

  • The elements of params_knn_defaults(), overridden by knn, spliced in at this position.