Wrapper function for parameters for neighbour identification in single cell

Usage

params_sc_neighbours(
  full_snn = FALSE,
  pruning = 1/15,
  snn_similarity = c("rank", "jaccard"),
  knn = list()
)

full_snn: Boolean. Shall the full shared nearest neighbour graph be generated that generates edges between all cells instead of between only neighbours.
pruning: Numeric. Weights below this threshold will be set to 0 in the generation of the sNN graph.
snn_similarity: String. One of c("rank", "jaccard"). The Jaccard similarity calculates the Jaccard between the neighbours, whereas the rank method calculates edge weights based on the ranking of shared neighbours. For the rank method, the weight is determined by finding the shared neighbour with the lowest combined rank across both cells, where lower-ranked (closer) shared neighbours result in higher edge weights Both methods produce weights normalised to the range [0, 1].
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.

A list with the neighbour parameters.