Generics of these functions are defined in SpatialExperiment
, except
for transposeImg
. These SFE methods cater to the new image-related
classes in SFE. The SPE method for getImg
, rmvImg
, and
imgRaster
don't need to be modified for SFE and are hence not
implemented here, but are simply re-exported.
Usage
# S4 method for SpatialFeatureExperiment
addImg(
x,
imageSource,
sample_id = 1L,
image_id,
extent = NULL,
scale_fct = 1,
file = deprecated()
)
# S4 method for SpatialFeatureExperiment
transposeImg(
x,
sample_id = 1L,
image_id = NULL,
maxcell = 1e+07,
filename = ""
)
# S4 method for SpatialFeatureExperiment
mirrorImg(
x,
sample_id = 1L,
image_id = NULL,
direction = "vertical",
maxcell = 1e+07,
filename = ""
)
# S4 method for SpatialFeatureExperiment
rotateImg(x, sample_id = 1L, image_id = NULL, degrees, maxcell = 1e+07)
# S4 method for SpatialFeatureExperiment
translateImg(x, sample_id = 1L, image_id = NULL, v)
# S4 method for SpatialFeatureExperiment
scaleImg(x, sample_id = 1L, image_id = NULL, factor)
# S4 method for SpatialFeatureExperiment
affineImg(x, sample_id = 1L, image_id = NULL, M, v)
Arguments
- x
A SFE object.
- imageSource
a character string specifying an image file name (.png, .jpg or .tif) or URL to source the image from
- sample_id
Which sample the image is associated with. Use
sampleIDs
to get sample IDs present in the SFE object.- image_id
Image ID, such as "lowres" and "hires" for Visium data and "DAPI" and "PolyT" for Vizgen MERFISH data.
- extent
A numeric vector of length 4 with names of the set xmin, ymin, xmax, and ymax, specifying the extent of the image.
- scale_fct
Scale factor -- multiply pixel coordinates in full resolution image by this scale factor should yield pixel coordinates in a different resolution.
extent
takes precedence overscale_fct
.- file
File from which to read the image.
- maxcell
Max number of pixels to load
SpatRasterImage
into memory. The default 1e7 is chosen because this is the approximate number of pixels in the medium resolution image atresolution = 4L
in Xenium OME-TIFF to make different methods of this function consistent.- filename
character. Output filename
- direction
character. Should (partially) match "vertical" to flip by rows, or "horizontal" to flip by columns
- degrees
How many degrees to rotate. Positive number means clockwise and negative number means counterclockwise.
- v
A numeric vector of length 2 specifying the vector in the xy plane to translate the SFE object.
- factor
Numeric, scaling factor.
- M
A 2x2 numeric matrix for the linear transformation in the xy plane.
Details
Method of transposeImg
, mirrorImg
, and
rotateImg
perform the method on all images within the SFE
object that are specified with sample_id
and image_id
. For
images that are not loaded into memory, rotateImg
will load
SpatRasterImage
into memory and all image operations except translate
will load BioFormatsImage
into memory.
Note
If the image is already a GeoTIFF file that already has an extent, then
the extent associated with the file will be honored and the extent
and
scale_fct
arguments are ignored. Transposing the image is just like
transposing a matrix. It's flipped about the line going from the top left to
the bottom right.
See also
Other image methods:
affineImg()
,
cropImg()
,
dim,BioFormatsImage-method
,
ext()
,
imgRaster()
,
imgSource()
,
mirrorImg()
,
rotateImg()
,
scaleImg()
,
translateImg()
,
transposeImg()
Examples
library(SFEData)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
img_path <- system.file(file.path("extdata", "sample01", "outs", "spatial",
"tissue_lowres_image.png"), package = "SpatialFeatureExperiment")
sfe <- addImg(sfe, img_path, sample_id = "Vis5A", image_id = "lowres", scale_fct =
0.023)
img <- getImg(sfe)
# SpatRasterImage method
img_t <- transposeImg(img)
# SFE method
sfe <- transposeImg(sfe, sample_id = "Vis5A", image_id = "lowres")