mergeWithTissueOutline.Rd
Ensures that the outline of a spatial annotation does not transgresses the outline of the tissue.
mergeWithTissueOutline(object, id, new_id)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Character value. The ID of the spatial annotation whose outline is supposed to be cut at the tissue edge.
If character, gives the resulting spatial annotation a new
id. If NULL
, the spatial annotation is overwritten!
The updated input object, containing the added, removed or computed results.
library(SPATA2)
data("example_data")
object <- loadExampleObject("UKF313T")
if(!containsTissueOutline(object)){
object <- identifyTissueOutline(object)
}
# image annotation which transgresses the tissue edge
plotSpatialAnnotations(object, ids = c("necrotic_edge2_transgr"))
object <-
mergeWithTissueOutline(object, id = "necrotic_edge2_transgr", new_id = "necrotic_edge2", overwrite = TRUE)
plotSpatialAnnotations(object, ids = c("necrotic_edge2_transgr", "necrotic_edge2"))