useVarForTissueOutline: Use specified variable for tissue outline

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Use specified variable for tissue outline

Description

This function sets a specified variable from the metadata of the given object to be used if identifyTissueOutline() does not produce acceptable results.

Usage

useVarForTissueOutline(
  object,
  var_name,
  concavity = 2,
  min_obs = nObs(object) * 0.05
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
var_name	A character string specifying the name of the variable in the metadata to be used for the tissue outline.
concavity	Numeric value. Given to argument concavity of concaveman::concaveman(). Determines the relative measure of concavity. 1 results in a relatively detailed shape, Infinity results in a convex hull. You can use values lower than 1, but they can produce pretty crazy shapes.
min_obs	Numeric value. The minimal number of observations a group must have to be considered a tissue section. Defaults to 5% of the total number of observations. Must be higher than 3.

Value

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

See Also

createSpatialSegmentation() to create the outline manually, then use the created spatial segmentation variable as input for var_name.

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