SFE-image | R Documentation |
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.
## S4 method for signature 'SpatialFeatureExperiment'
addImg(
x,
imageSource,
sample_id = 1L,
image_id,
extent = NULL,
scale_fct = 1,
file = deprecated()
)
## S4 method for signature 'SpatialFeatureExperiment'
transposeImg(
x,
sample_id = 1L,
image_id = NULL,
maxcell = 1e+07,
filename = ""
)
## S4 method for signature 'SpatialFeatureExperiment'
mirrorImg(
x,
sample_id = 1L,
image_id = NULL,
direction = "vertical",
maxcell = 1e+07,
filename = ""
)
## S4 method for signature 'SpatialFeatureExperiment'
rotateImg(x, sample_id = 1L, image_id = NULL, degrees, maxcell = 1e+07)
## S4 method for signature 'SpatialFeatureExperiment'
translateImg(x, sample_id = 1L, image_id = NULL, v)
## S4 method for signature 'SpatialFeatureExperiment'
scaleImg(x, sample_id = 1L, image_id = NULL, factor)
## S4 method for signature 'SpatialFeatureExperiment'
affineImg(x, sample_id = 1L, image_id = NULL, M, v)
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
|
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. |
file |
File from which to read the image. |
maxcell |
Max number of pixels to load |
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. |
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.
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.
Other image methods:
affineImg()
,
cropImg()
,
dim,BioFormatsImage-method
,
ext()
,
imgRaster()
,
imgSource()
,
mirrorImg()
,
rotateImg()
,
scaleImg()
,
translateImg()
,
transposeImg()
library(SFEData)
sfe <- McKellarMuscleData("small")
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")
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