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Helper function to generate kNN data with distances

new_sc_knn.Rd

Wrapper class that stores kNN data for subsequent usage in various other functions, methods and helpers.

Usage

new_sc_knn(knn_data, used_cells)

Arguments

knn_data

Named list with the following items:

  • indices - Integer matrix containing the indices of the nearest neighbours (0-indexed).

  • dist - Numerical matrix containing the distances to the nearest neighbours.

  • dist_metric - String. Distance metric used.

used_cells

Character vector. The cells used to generate the kNN graph with the distances.

Value

Generates the SingleCellNearestNeighbour class.

Examples

# rebuild the kNN wrapper from an existing graph
sc <- demo_single_cells()
knn <- generate_knn_sc(sc, .validate_index = FALSE, .verbose = FALSE)
new_sc_knn(
  knn_data = list(
    indices = get_knn_mat(knn),
    dist = get_knn_dist(knn),
    dist_metric = "euclidean"
  ),
  used_cells = get_cell_names(sc)
)
#> SingleCellNearestNeighbour: 500 cells, k = 15
#>   Distance metric: euclidean
#>   Index range: [0, 499]
#>   Distance range: [1.1849, 4.2876]

unlink(sc@dir_data, recursive = TRUE, force = TRUE)