Build a k-nearest-neighbour graph between cells

Finds the k nearest neighbours of every cell within its own image and stores them as a colPair of cells, ready for convPairs(). Distances are Euclidean, a cell is not its own neighbour, and ties are broken as in spatstat.geom::nnwhich(). The graph is the one imcRtools::buildSpatialGraph(type = "knn") builds, computed by the C++ core that spicy() uses for k.

Usage

buildKnnGraph(
  cells,
  k = 20,
  imageID = "imageID",
  spatialCoords = c("x", "y"),
  name = "knn_interaction_graph",
  cores = 1
)

Arguments

cells

A SingleCellExperiment or SpatialExperiment.

k

The number of neighbours of each cell. Cells in images with at most k cells get no neighbours.

imageID

The colData column holding the image of each cell.

spatialCoords

The colData columns holding the coordinates. A SpatialExperiment's own spatialCoords() are used unless these name colData columns.

name

The name of the colPair the graph is stored in.

cores

The number of threads; images are processed in parallel.

Value

cells, with the graph in colPair(cells, name): one edge from each cell to each of its neighbours.

Examples

data("diabetesData")
diabetesData <- buildKnnGraph(diabetesData, k = 10)
head(SingleCellExperiment::colPair(diabetesData, "knn_interaction_graph"))
#> SelfHits object with 6 hits and 0 metadata columns:
#>            from        to
#>       <integer> <integer>
#>   [1]         1         6
#>   [2]         1        11
#>   [3]         1        12
#>   [4]         1        20
#>   [5]         1        59
#>   [6]         1        66
#>   -------
#>   nnode: 253777