SFE-image: Images in SpatialFeatureExperiment object

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

Images in SpatialFeatureExperiment object

Description

SpatialFeatureExperiment and the Voyager package work with images differently from SpatialExperiment. In SFE and Voyager's, plotting functions for SFE objects, the images are read with rast and represented as SpatRaster, so the image is not entirely loaded into memory unless necessary. Plotting will not load a large image into memory; rather the image will be downsampled and the downsampled version is plotted.

Usage

## S4 method for signature 'SpatialFeatureExperiment'
addImg(x, file, sample_id, image_id, extent = NULL, scale_fct = 1)

## S4 method for signature 'SpatRasterImage'
transposeImg(x)

## S4 method for signature 'SpatRasterImage'
mirrorImg(x, direction = "vertical")

## S4 method for signature 'SpatialFeatureExperiment'
transposeImg(x, sample_id = NULL, image_id = NULL)

## S4 method for signature 'SpatialFeatureExperiment'
mirrorImg(x, sample_id = NULL, image_id = NULL, direction = "vertical")

## S4 method for signature 'SpatRasterImage'
imgRaster(x)

## S4 method for signature 'SpatRasterImage'
imgSource(x)

Arguments

x	SpatRaster or SpatVector
file	File from which to read the image.
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.
direction	character. Should (partially) match "vertical" to flip by rows, or "horizontal" to flip by columns

Value

Methods for SpatRasterImage return a modified SpatRasterImage, and methods for SFE return a modified SFE object.

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. Also, when the image is transposed, it is flipped about the axis going from top left to bottom right.

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 March 11, 2024, 11:11 p.m.