imgData-methods: Methods for handling image-related data

In drighelli/VisiumExperiment: S4 Class for Spatially Resolved -omics Data

Methods for handling image-related data

Description

The set of functions described below is designed to handle the image-related data stored inside a SpatialExperiment's imgData int_metadata field. These include:

• getImg, addImg, rmvImg to retrieve/add/remove an image entry to/from the imgData DataFrame

• imgSource, imgRaster to retrieve the path/URL and raster object, respectively, associated with an image or set of images

Usage

## S4 method for signature 'SpatialExperiment'
getImg(x, sample_id = NULL, image_id = NULL)

## S4 method for signature 'SpatialExperiment'
addImg(x, imageSource, scaleFactor, sample_id, image_id, load = TRUE)

## S4 method for signature 'SpatialExperiment'
rmvImg(x, sample_id = NULL, image_id = NULL)

## S4 method for signature 'SpatialExperiment'
imgSource(x, sample_id = NULL, image_id = NULL, path = FALSE)

## S4 method for signature 'SpatialExperiment'
imgRaster(x, sample_id = NULL, image_id = NULL)

## S4 method for signature 'SpatialExperiment'
rotateImg(x, sample_id = NULL, image_id = NULL, degrees = 90)

## S4 method for signature 'SpatialExperiment'
mirrorImg(x, sample_id = NULL, image_id = NULL, axis = c("h", "v"))

Arguments

x	a SpatialExperiment
sample_id	character string, TRUE or NULL specifying sample/image identifier(s); here, TRUE is equivalent to all samples/images and NULL specifies the first available entry (see details)
image_id	see sample_id
imageSource	a character string specifying an image file name (.png, .jpg or .tif) or URL to source the image from
scaleFactor	single numeric scale factor used to rescale spatial coordinates according to the image's resolution
load	logical; should the image(s) be loaded into memory as a raster object? if FALSE, will store the path/URL instead
path	logical; for RemoteSpatialImages, TRUE returns the path to the image's cached file, and FALSE its URL. For Stored/LoadedSpatialImages, a path/NA is returned, irrespective of path.
degrees	single numeric in +/-[0,90,...,360] specifying how many degrees to rotate. A negative/positive value corresponds to counter-/clockwise rotation
axis	character string specifying whether to mirror horizontally ("h") or vertically ("v")

Value

getImg() returns a single or list of SpatialImage(s).

add/rmvImg() return a SpatialExperiment with modified imgData; specifically, they create/remove an image entry (row) in the imgData DataFrame.

imgRaster/Source() access relevant data in the SpatialImage(s) stored inside the imgData's data field. Depending on whether or not multiple entries are accessed, a character string or vector is returned by imgSource(), and a single or list of raster object(s) is returned by imgRaster().

rotate/mirrorImg() return a LoadedSpatialImage with modified a raster matrix.

Author(s)

Helena L. Crowell

Examples

example(read10xVisium)

# 'SpatialImage' accession
(spi <- getImg(spe))
plot(imgRaster(spi))

# remove an image
imgData(spe)
spe <- rmvImg(spe,
  sample_id = "section1",
  image_id = "lowres")
imgData(spe)

# add an image
url <- "https://i.redd.it/3pw5uah7xo041.jpg"
spe <- addImg(spe,
  sample_id = "section1",
  image_id = "pomeranian",
  imageSource = url,
  scaleFactor = NA_real_,
  load = FALSE)

# extract image
img <- imgRaster(spe,
  sample_id = "section1",
  image_id = "pomeranian")
plot(img)

###################
# transformations #
###################

# clockwise rotation
spe1 <- rotateImg(spe, 
  degrees = 90) # first image
  
spe2 <- rotateImg(spe, 
  sample_id = TRUE,
  image_id = TRUE, 
  degrees = 90) # all images

par(mfrow = c(1, 3))
plot(imgRaster(spe))
plot(imgRaster(spe1))
plot(imgRaster(spe2))

# horizontal/vertical mirroring
spe1 <- mirrorImg(spe, axis = "h")
spe2 <- mirrorImg(spe, axis = "v")

par(mfrow = c(1, 3))
plot(imgRaster(spe))
plot(imgRaster(spe1))
plot(imgRaster(spe2))
  

drighelli/VisiumExperiment documentation built on April 10, 2024, 8:01 a.m.