imgData-methods {SpatialExperiment} | R Documentation |
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
## 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)
x |
|
sample_id |
character string, |
image_id |
see |
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 |
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()
.
Helena L. Crowell
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)