getTissueOutlineDf: Obtain the outline of tissue sections

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain the outline of tissue sections

Description

Extracts the polygons necessary to outline the tissue. See vignette about tissue outline for more information.

Usage

getTissueOutlineDf(object, ...)

## S4 method for signature 'SPATA2'
getTissueOutlineDf(
  object,
  method = "obs",
  img_name = activeImage(object),
  by_section = TRUE,
  section_subset = NULL,
  transform = TRUE,
  ...
)

## S4 method for signature 'SpatialData'
getTissueOutlineDf(
  object,
  method = NULL,
  img_name = activeImage(object),
  by_section = TRUE,
  section_subset = NULL,
  transform = TRUE
)

## S4 method for signature 'HistoImage'
getTissueOutlineDf(
  object,
  by_section = TRUE,
  section_subset = NULL,
  transform = TRUE
)

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.
method	Character value. Either 'obs' or 'image'. Decides whether the tissue outline used based on the observations or the image is used. If method = NULL, the function checks first if any HistoImage is registered. If so, the outline from the image specified with img_name is returned. If there are no images, the outline computed with identifyTissueOutline(..., method = 'obs') is used.
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().
by_section	Logical value. If TRUE, the outline is used which acknowledges the potential for multiple tissue sections. If FALSE, the outline is used which simply outlines everything with one single polygon.
section_subset	Character vector or NULL. If character, specifies the tissue sections of interest and filters the output accordingly.
transform	Logical value. Ignored if no images exist in the object. If TRUE, spatial transformation instructions saved during image alignment of the image img_name are applied. Only relevant if there are any images registered in the SPATA2 object.

Value

Data.frame of vertices with x- and y-coordinates. If by_section = TRUE, the data.frame contains an additional variable which indicates the tissue section which the polygon to which the vertex belongs outlines.

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