Add histology image — ggpLayerImage • SPATA2

Creates ggplot2 layer with the histology image as a raster.

ggpLayerImage(object, ...)

# S4 method for class 'SPATA2'
ggpLayerImage(
  object,
  img_name = activeImage(object),
  transform = TRUE,
  img_alpha = 1,
  scale_fct = 1,
  ...
)

# S4 method for class 'SpatialData'
ggpLayerImage(
  object,
  img_name = activeImage(object),
  transform = TRUE,
  img_alpha = 1,
  scale_fct = 1,
  ...
)

# S4 method for class 'HistoImage'
ggpLayerImage(object, transform = TRUE, scale_fct = 1, img_alpha = 1, ...)

# S4 method for class 'SpatialAnnotation'
ggpLayerImage(object, img_alpha = 1, rescale_axes = TRUE, scale_fct = 1, ...)

# S4 method for class 'Image'
ggpLayerImage(object, scale_fct = 1, img_alpha = 1, ...)

# S4 method for class 'data.frame'
ggpLayerImage(object, fill_by, img_alpha = 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.
img_alpha: Numeric value. Sets the transparency for the image.

Value

ggpLayer*()-functions return lists of ggproto objects that can be added to ggplots via the + operator. In most of the cases they are supposed to be added to plots created with the plotSurface*() family.

Details

The image is plotted via ggplot2::geom_raster() by mapping the pixel position to the x-axis and the y-axis. See section Image visualization with ggplot2 for more details.

Image visualization with ggplot2

When comparing the output of ggplot() + ggpLayerImage() with other image plotting functions, you may notice that the image appears horizontally flipped when plotted using ggpLayerImage(). This behavior is due to the use of a Cartesian coordinate system in SPATA2, where a pixel with coordinates c(width = 1, height = 1) is plotted on the left side at the bottom. In contrast, functions like EBImage::display() or graphics::plot() use an image space coordinate system, where pixel heights start from the top. Consequently, in image space, pixel c(width = 1, height = 1) is displayed on the top resulting in mirror inverted visualization of the image.

We chose to use a Cartesian coordinate system in SPATA2 because we believe it provides a more intuitive framework for the spatial alignment of tissue, spatial annotations, spatial trajectories, barcoded sots, single cells, etc. where coordinates in the corresponding data.frames are provided in form of x- and y-variables. See getCoordsDf(), getImgAnnOutlineDf(), getTissueOutlineDf() etc.

If you prefer to view your image in the regular orientation, you can use the flipAll() function on your object, specifying axis = "horizontal", to reverse this effect.

Examples


library(SPATA2)
library(tidyverse)

data("example_data")

object <- loadExampleObject("UKF275T")

ggplot() +
 ggpLayerImage(object)