crop: Crop an SFE object with a geometry

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

Crop an SFE object with a geometry

Description

Returns an SFE object whose specified colGeometry returns TRUE with a geometric predicate function (usually intersects) with another geometry of interest. This can be used to subset an SFE object with a tissue boundary or histological region polygon, or crop away empty spaces. After cropping, not only will the cells/spots be subsetted, but also all geometries will be cropped.

Usage

crop(
  x,
  y = NULL,
  colGeometryName = 1L,
  sample_id = "all",
  pred = deprecated(),
  op = st_intersection,
  keep_whole = "none",
  cover = FALSE,
  xmin = deprecated(),
  xmax = deprecated(),
  ymin = deprecated(),
  ymax = deprecated()
)

Arguments

x	An SFE object.
y	An object of class sf, sfg, sfc with which to crop the SFE object, or a bounding box with the format of the output of bbox,SpatialFeatureExperiment-method.
colGeometryName	Column geometry to used to indicate which cells/spots to keep.
sample_id	Samples to crop. Optional when only one sample is present. Can be multiple samples, or "all", which means all samples. For multiple samples, sf data frame y may have column sample_id indicating which geometry subsets which sample or matrix y may indicate sample specific bounding boxes in its column names. Only samples included in the indicated sample IDs are subsetted. If sample is not indicated in y, then the same geometry or bounding box is used to subset all samples specified in the sample_id argument.
pred	Deprecated. The binary predicate is now tied to the geometric operation specified in op.
op	A geometric operation function to crop the geometries in the SFE object. Only st_intersection and st_difference are allowed. If "intersection", then only things inside y is kept after cropping. If "difference", then only things outside y is kept.
keep_whole	Character vector, can be one or more of "col" and "annot" to keep whole items from colGeometries or annotGeometries, keeping geometries that partially intersect with y whole. This can greatly speed up code while not breaking geometries into multiple pieces. Can also be "none" so all geometries are actually cropped.
cover	Logical, whether the geometries in x must be entirely covered by y if op = st_intersection or whether x must be entirely outside y if op = st_difference. Only relevant when keep_whole != "none".
xmin	Deprecated. Supply the bounding box to argument y instead.
xmax	Deprecated.
ymin	Deprecated.
ymax	Deprecated.

Details

3D geometries are allowed, but geometric operations can only be performed in x and y but not z.

Value

An SFE object. There is no guarantee that the geometries after cropping are still all valid or preserve the original geometry class.

Examples

library(SFEData)
sfe <- McKellarMuscleData("small")
# Subset sfe to only keep spots on tissue
sfe_on_tissue <- crop(sfe, tissueBoundary(sfe),
    colGeometryName = "spotPoly",
    sample_id = "Vis5A"
)

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.