shiftSpatialAnnotation: Shift the borders of a spatial annotation

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Shift the borders of a spatial annotation

Description

This function moves a spatial annotation either in the x or y direction, or both. It allows for selective shifting of outer and/or inner borders of the annotation.

Usage

shiftSpatialAnnotation(
  object,
  id,
  outer = TRUE,
  inner = TRUE,
  shift_x = 0,
  shift_y = 0,
  new_id = FALSE,
  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.
id	Character value specifying the ID of the spatial annotation of interest. If there is only one spatial annotation in the object, the function will default to using it. However, if there are multiple annotations, this argument must be explicitly specified to identify the target annotation.
outer	Logical; if TRUE, the outer border of the annotation is affected.
inner	Logical or numeric; if TRUE, all inner borders are affected. If a numeric value is provided, only the specified inner borders are affected.
shift_x, shift_y	Distance measure. The shift in the x- and/or y-direction. Negative values are also accepted.
new_id	Character value or FALSE. If character, the resulting spatial annotation is stored under a new ID.
overwrite	Logical value. Must be TRUE to allow overwriting.

Value

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

See Also

expandSpatialAnnotation(), smoothSpatialAnnotation(), SpatialAnnotation

Examples

library(SPATA2)
library(patchwork)
library(stringr)

data("example_data")

object <- example_data$object_UKF313T_diet

p1 <- plotImage(object) + ggpLayerSpatAnnOutline(object, ids = "necrotic_area")

plot(p1)

object <- shiftSpatialAnnotation(object, id = "necrotic_area", shift_x = "0.5mm", shift_y = "0.25mm", new_id = "na_shifted")

p2 <- plotImage(object) + ggpLayerSpatAnnOutline(object, ids = "na_shifted")

# compare both
p1 + p2

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