Convert SingleCellNearestNeighbour to manifoldsR NearestNeighbours

Converts the bixverse single cell kNN class into the manifoldsR NearestNeighbours class for use in UMAP, tSNE, etc. Note that the bixverse class stores 0-indexed indices whereas manifoldsR expects 1-indexed, so the conversion handles that.

Usage

sc_knn_to_nearest_neighbours(x)

Arguments

x

SingleCellNearestNeighbour class.

Value

A NearestNeighbours class compatible with manifoldsR.

Examples

# hand the single cell kNN graph over to manifoldsR
sc <- demo_single_cells()
knn <- generate_knn_sc(sc, .validate_index = FALSE, .verbose = FALSE)
sc_knn_to_nearest_neighbours(knn)
#> NearestNeighbours
#>   n_samples:    500 
#>   k_neighbours: 15 

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