add_images: Add non-standard images with the same dimensions as current...

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Add non-standard images with the same dimensions as current ones

Description

This function re-uses the SpatialExperiment::scaleFactors() from current images when adding new images. This is useful if you take for example a multi-channel VisiumIF image and break into several single-channel images that all have the same dimensions. So you could have a set of images such as channel_01_lowres and channel_02_lowres that have the same dimensions and viewing area as the lowres image produced by SpaceRanger, each with only one channel. Similarly, you might have done some image manipulation for a given image and generated one or more images with the same dimensions as existing images.

Usage

add_images(
  spe,
  image_dir,
  image_pattern,
  image_id_current = "lowres",
  image_id = image_pattern,
  image_paths = locate_images(spe, image_dir, image_pattern)
)

Arguments

spe	A SpatialExperiment-class object. See fetch_data() for how to download some example objects or read10xVisiumWrapper() to read in spaceranger --count output files and build your own spe object.
image_dir	A character(1) specifying a path to a directory containing image files with the pattern sampleID_pattern.png.
image_pattern	A character(1) specifying the pattern for the image files.
image_id_current	A character(1) specifying the name of the current existing image in spe that has the same scaling factor that to be used with the additional images.
image_id	A character(1) specifying the name to use in the new images. It cannot be the same as one used for existing images in spe for a given sample. It equals image_pattern by default.
image_paths	A named character() vector with the paths to the images. The names have to match the spe$sample_id and cannot be repeated. By default locate_images() is used but you can alternatively specify image_paths and ignore image_dir and image_pattern.

Value

A SpatialExperiment-class object with the additional image data in imgData(spe).

See Also

Other Functions for adding non-standard images: locate_images()

Examples

if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Add an image
    SpatialExperiment::imgData(add_images(
        spe,
        image_id_current = "lowres",
        image_id = "lowres_aws",
        image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
    ))
}

LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 a.m.