img_update_all: Update the images for all samples

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

Update the images for all samples

Description

This function uses img_update() for all samples. That is, it loops through every sample and edits the image with img_edit() and then updates the imgData().

Usage

img_update_all(
  spe,
  image_id = "lowres",
  new_image_id = paste0("edited_", image_id),
  overwrite = FALSE,
  ...
)

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_id	A character(1) with the name of the image ID you want to use in the background.
new_image_id	A character(1) specifying the new image_id to use.
overwrite	A logical(1) specifying whether to overwrite the image_id if it already exists.
...	Parameters passed to img_edit().

Value

A SpatialExperiment-class object with an updated imgData() slot.

See Also

Other Image editing functions: img_edit(), img_update()

Examples

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

    ## Reduce brightness to 25% for the 'lowres' image for all samples and
    ## update the imgData()
    imgData(img_update_all(spe, brightness = 25))
}

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