getSpatAnnArea: Obtain area of spatial annotation

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain area of spatial annotation

Description

Computes the area of spatial annotations.

Usage

getSpatAnnArea(object, ...)

## S4 method for signature 'SPATA2'
getSpatAnnArea(
  object,
  ids = NULL,
  unit = "mm2",
  tags = NULL,
  test = "any",
  as_numeric = TRUE,
  verbose = NULL,
  ...
)

## S4 method for signature 'SpatialData'
getSpatAnnArea(
  object,
  ids = NULL,
  tags = NULL,
  test = "any",
  unit = "mm2",
  as_numeric = TRUE,
  verbose = NULL,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Used to absorb deprecated arguments or functions.
unit	Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.
tags	Character vector or NULL. If character, the tags for the image annotation selection. See section Selection of spatial annotations for more information.
test	Character value. One of c('any'. 'all', 'identical', 'not_identical', 'none'). Specifies how input for tags is used to select spatial annotations. See section Selection of spatial annotations for more information.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

Contains the area of the spatial annotations in the unit that is specified in unit. The unit is attached to the output as an attribute named unit. E.g. if ⁠unit = *mm2*⁠ the output value has the unit mm^2.

Note

The area is computed solely based on the outline of the annotation even if the annotation transgresses the tissue outline! If you only want the area of the annotation on the tissue section adjust the annotation with mergeWithTissueOutline(). See examples.

See Also

getSpatAnnOutlineDf(), getCCD(), as_unit()

Examples

library(SPATA2)

object <- loadExampleObject("UKF313T")

ids <- c("necrotic_edge2", "necrotic_edge2_transgr")

plotSpatialAnnotations(object, ids = ids)

getSpatAnnArea(object, ids = ids)

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