Find the k-th nearest cells for each cell

Find the k-th nearest cells for each cell

Usage

findNearCells(
  dat,
  k = 100,
  targetCell = FALSE,
  reportCellID = FALSE,
  reportDist = TRUE,
  anno_col = 0
)

Arguments

dat

A SpatialExperiment object, can be generated using function readHoodData.

k

The maximum number of nearest cells to compute.

targetCell

Specify the cells to be the target cell for finding nearest cells.

reportCellID

Logical. Set to TRUE to report cell id instead of cell types.

reportDist

Logical. Set to TRUE to report the distance matrix.

anno_col

Character vector. The name of annotation column to use.

Value

A list includes a data.frame and a matrix, describing the cell types and distances of the k-th nearest cells of each cell.

Details

The findNearCells function uses the nn2 function from the RANN package, which uses the Approximate Near Neighbor (ANN) C++ library. For more infromation on the ANN library please see http://www.cs.umd.edu/~mount/ANN/.

Examples

data("spe_test")

spe <- readHoodData(spe, anno_col = "celltypes")

fnc <- findNearCells(spe, k = 100)