annotOp: Binary operations for geometry of each cell/spot and...

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Binary operations for geometry of each cell/spot and annotation

Description

Just like annotPred, but performs the operation rather than predicate. For example, this function would return the geometry of the intersections between each Visium spot and the tissue boundary for each sample, rather than whether each Visium spot intersects the tissue boundary. In case one cell/spot gets broken up into multiple geometries, the union of those geometries will be taken, so each cell/spot will only get one geometry.

Usage

annotOp(
  sfe,
  colGeometryName = 1L,
  annotGeometryName = 1L,
  sample_id = "all",
  op = st_intersection
)

Arguments

sfe	An SFE object.
colGeometryName	Name of column geometry for the predicate.
annotGeometryName	Name of annotation geometry for the predicate.
sample_id	Which sample(s) to operate on. Can be "all" to indicate all samples.
op	A binary operation function for the geometries. Defaults to st_intersection.

Value

A sf data frame with geometry column containing the geometries and corresponding column names of sfe as row names. There is no guarantee that the returned geometries are valid or preserve the geometry class (e.g. when the intersection of polygons result into a line of a point).

See Also

annotPred

Examples

library(SFEData)
sfe <- McKellarMuscleData("small")
# Get the intersection of myofibers with each Visium spot
myofibers_on_spots <- annotOp(sfe, "spotPoly",
    annotGeometryName = "myofiber_simplified"
)

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.