getImageDf: Obtain image as a data.frame

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain image as a data.frame

Description

Extracts a data.frame in which each row corresponds to a pixel in the image. (Faster than getPixelDf(), though without any further options.)

Usage

getImageDf(object, ...)

## S4 method for signature 'SPATA2'
getImageDf(
  object,
  img_name = activeImage(object),
  transform = TRUE,
  scale_fct = 1,
  ...
)

## S4 method for signature 'SpatialData'
getImageDf(
  object,
  img_name = activeImage(object),
  transform = TRUE,
  scale_fct = 1
)

## S4 method for signature 'HistoImage'
getImageDf(object, transform = TRUE, scale_fct = 1)

## S4 method for signature 'SpatialAnnotation'
getImageDf(object, rescale_axes = TRUE, scale_fct = 1)

## S4 method for signature 'Image'
getImageDf(object, scale_fct = 1)

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.
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().
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.
rescale_axes	Logical value. If TRUE, rescales the pixel positions (height/width) to the position in the original image. The image annotation contains a crop of the original image that only shows the area of the image annotation (plus expand, see getSpatialAnnotation()).

Value

Data.frame with three variables.

• width: Numeric. Width value of the pixel (position on horizontal axis).

• height: Numeric. Height value of the pixel (position on vertical axis).

• color: Character. HEX-code of the color the pixel carries.

See Also

getPixelDf()

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