Find bounding box of SFE objects
Source:R/geometry_operation.R
bbox-SpatialFeatureExperiment-method.Rd
Find bounding box of the union of all colGeometries
and
annotGeometries
of each sample in the SFE object. This can be used to
remove empty space so the tissue and geometries have one corner at the origin
so all samples will be on comparable coordinates.
Usage
# S4 method for class 'SpatialFeatureExperiment'
bbox(sfe, sample_id = "all", include_images = FALSE, include_row = TRUE)
Arguments
- sfe
A
SpatialFeatureExperiment
object.- sample_id
Sample(s) whose bounding box(es) to find. The bounding box would be for the union of all
colGeometries
andannotGeometries
associated with each sample.- include_images
Logical, whether the bounding boxes should include image extents. Defaults to
FALSE
because often the image has a lot of empty space surrounding the tissue.- include_row
Logical, whether the bounding boxes should include
rowGeometries
, defaults toTRUE
.
Value
For one sample, then a named vector with names xmin
,
ymin
, xmax
, and ymax
specifying the bounding box. For
multiple samples, then a matrix whose columns are samples and whose rows
delineate the bounding box.
Examples
library(SFEData)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
bbox(sfe, sample_id = "Vis5A")
#> xmin ymin xmax ymax
#> 5000 13000 7000 15000