getTissueArea: Obtain tissue area size

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain tissue area size

Description

Computes and extracts the size of the area covered by the tissue.

Usage

getTissueArea(object, unit, method = "obs", img_name = activeImage(object))

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
unit	Character value. Output unit. Must be one of validUnitsOfArea().
method	Character value. Defines the origin based on which the outline is computed. Either 'image' or 'obs'.
img_name	Character value. The name of the image of interest. If NULL, the active image is chosen by default. Either way, must be one of getImageNames().

Value

A vector of area measures. Length is equal to the number of tissue sections.

See Also

getTissueSections(), identifyTissueOutline()

Examples

library(SPATA2)

## Example 1 - image based
object <- example_data$object_UKF313T_diet

object <- identifyPixelContent(object)
object <- identifyTissueOutline(object, method = "image")

plotImage(object, outline = TRUE) +
 ggpLayerAxesSI(object, unit = "mm")

getTissueArea(object, unit = "mm")

## Example 2 - coordinates based
object <- loadExampleObject("UKF313T")

object <- identifyTissueOutline(object, method = "obs")

plotSurface(object, color_by = "tissue_section") +
 ggpLayerTissueOutline(object)

area_out <- getTissueArea(object)

print(area_out)

sum(area_out)

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