SFE-image: Methods for handling image-related data

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Methods for handling image-related data

Description

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 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)

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 over scale_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 at resolution = 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")
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")

pachterlab/SpatialFeatureExperiment documentation built on Aug. 5, 2024, 8:36 a.m.