createHistologyImaging: Create object of class 'HistologyImaging'

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Create object of class HistologyImaging

Description

Creates an object of class HistologyImaging that is used to store the image, image meta data and image annotations.

Located in slot @images in the SPATA2 object.

Usage

createHistologyImaging(
  image,
  id = "imageid",
  img_scale_fct = 1,
  meta = list(),
  pxl_scale_fct = NULL,
  coordinates = NULL,
  verbose = TRUE,
  ...
)

Arguments

image	Image input or character value. If character, input is interpreted as a directory to a file or to an URL and is read with EBImage::readImage(). The read image should be of type .png, .jpeg or .tiff. Capital letters work, too. If not character, the function ensures that the input is - or is convertible - to class Image via EBImage::as.Image(). If that fails, an error is thrown.
id	Character value. Name of the HistologyImaging object.
img_scale_fct	Numeric value between 0 and 1. If lower than 1, is used to downscale the image before setting it.
coordinates	A data.frame of observational units that underlie the image in case of spatially resolved multi-omic studies. Should contain at least the two variables: x, y and a variable that identifies the observational units (e.g. barcodes).

Value

An object of class HistologyImaging.

See Also

?HistologyImaging for the documentation of all slots.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.