imgData-methods {SpatialExperiment}R Documentation

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:

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)

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

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

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().

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)
  

[Package SpatialExperiment version 1.4.0 Index]