Split by graph component

Split either a SFE object or sf or sfc by graph component of a spatial neighborhood graph.

Usage

# S4 method for class 'SpatialFeatureExperiment'
splitComponent(x, colGraphName = 1L, min_cells = 100)

# S4 method for class 'sf'
splitComponent(
  x,
  min_cells = 100,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

# S4 method for class 'sfc'
splitComponent(
  x,
  min_cells = 100,
  distance_cutoff = 50,
  BNPARAM = NULL,
  BPPARAM = SerialParam()
)

Arguments

x

A SFE object, or sf or sfc.

colGraphName

Name of graph to use for splitComponent. We recommend distance based neighbors (`dnearneigh` in findSpatialNeighbors), and recommend NOT using k nearest neighbors (`knearneigh`) or triangulation (`tri2nb`).

min_cells

Minimum number of cells per graph component; components with fewer than this number of cells are considered debris and removed.

distance_cutoff

For the sf and sfc methods, the distance cutoff used to construct a distance-based spatial neighborhood graph, in the same unit as the spatial coordinates. Anything within this distance is considered a neighbor.

BNPARAM

A BiocNeighborParam object specifying the algorithm to find k nearest neighbors and distance based neighbors with nn_method = "bioc". For distance based neighbors, only KmknnParam and VptreeParam are applicable.

BPPARAM

A BiocParallelParam object for multithreading. Only used for k nearest neighbor and distance based neighbor with nn_method = "bioc".

Value

A list of the same object type as the input, each element for one component.