Convert spatial annotation to grouping variable — spatialAnnotationToGrouping • SPATA2

Converts one or more spatial annotations to a binary segmentation variable in the feature data.frame.

spatialAnnotationToGrouping(
  object,
  ids,
  grouping_name,
  inside = "inside",
  outside = "outside",
  overwrite = FALSE
)

Arguments

object: An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
ids: Character vector. Specifies the spatial annotation(s) of interest. data points that fall into the area of these annotations are labeled with the input for argument inside.
grouping_name: Character value. The name of the new segmentation variable.
inside: Character value. The group name for the data points that are located inside the area of the spatial annotation(s).
outside: Character value. The group name for the data points that are located outside the area of the spatial annotation(s).
overwrite: Logical. Set to TRUE to overwrite existing variables with the same name.

Value

The updated input object, containing the added, removed or computed results.

Examples


library(SPATA2)
library(patchwork)

data("example_data")

object <- example_data$object_UKF313T_diet

ids <- getSpatAnnIds(object, tags = c("necrotic", "compr"), test = "all")

plotSpatialAnnotations(object, ids = ids)

object <-
  spatialAnnotationToGrouping(
    object = object,
    ids = ids,
    grouping_name = "histology",
    inside = "necrotic",
    outside = "vivid"
    )

plotSurface(object, color_by = "histology", clrp_adjust = c("necrotic" = "black", "vivid" = "forest_green"))