spatialAnnotationToGrouping: Convert spatial annotation to grouping variable

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Convert spatial annotation to grouping variable

Description

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

Usage

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"))

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.