getCoordsDf: Obtain coordinates

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain coordinates

Description

Extracts the coordinates data.frame of the identified or known entities the analysis revolves around.

Usage

getCoordsDf(object, ...)

## S4 method for signature 'SPATA2'
getCoordsDf(
  object,
  variables = NULL,
  img_name = activeImage(object),
  exclude = TRUE,
  as_is = FALSE,
  ...
)

## S4 method for signature 'SpatialData'
getCoordsDf(
  object,
  img_name = activeImage(object),
  scale = TRUE,
  exclude = TRUE,
  wh = FALSE,
  as_is = FALSE,
  ...
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Additional arguments given to joinWithVariables() if argument variables is specified.
variables	Character or NULL. If character, specifies the variables that are merged to the coordinates data.frame via joinWithVariables().
img_name	Only relevant if the SPATA2 object contains images. If so, specifies the name of the image to which the original coordinates are scaled. If NULL, defaults to the active image.
exclude	Logical. If TRUE, observations that are no longer part of the dataset (but still exist in the coordinates data frame for potential use in spatial computations) will be excluded and removed before returning the data frame.
as_is	Logical. If TRUE, no processing and coordinate scaling is conducted at all.

Value

Data.frame that, among others, contains at least the variables x_orig, y_orig and barcodes

See Also

activateImage(), activeImage()

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