img_edit: Edit a background image

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

Edit a background image

Description

This function uses the magick package to edit the color and perform other image manipulations on a background image. It can be useful if you want to highlight certain features of these images.

Usage

img_edit(
  spe,
  sampleid,
  image_id = "lowres",
  channel = NA,
  brightness = 100,
  saturation = 100,
  hue = 100,
  enhance = FALSE,
  contrast_sharpen = NA,
  quantize_max = NA,
  quantize_dither = TRUE,
  equalize = FALSE,
  normalize = FALSE,
  transparent_color = NA,
  transparent_fuzz = 0,
  background_color = NA,
  median_radius = NA,
  negate = FALSE
)

Arguments

spe	Defaults to the output of fetch_data(type = 'spe'). This is a SpatialExperiment-class object with the spot-level Visium data and information required for visualizing the histology. See fetch_data() for more details.
sampleid	A character(1) specifying which sample to plot from colData(spe)$sample_id (formerly colData(spe)$sample_name).
image_id	A character(1) with the name of the image ID you want to use in the background.
channel	A character(1) passed to magick::image_channel. If NA this step is skipped.
brightness	A numeric(1) passed to magick::image_modulate.
saturation	A numeric(1) passed to magick::image_modulate.
hue	A numeric(1) passed to magick::image_modulate.
enhance	A logical(1) controlling whether to use magick::enhance.
contrast_sharpen	A numeric(1) passed to magick::image_contrast. If NA this step is skipped.
quantize_max	A numeric(1) passed to magick::image_quantize. If NA this step is skipped.
quantize_dither	A logical(1) passed to magick::image_quantize.
equalize	A logical(1) controlling whether to use magick::equalize.
normalize	A logical(1) controlling whether to use magick::normalize.
transparent_color	A character(1) passed to magick::image_transparent. If NA this step is skipped.
transparent_fuzz	A numeric(1) passed to magick::image_transparent.
background_color	A character(1) passed to magick::image_background. If NA this step is skipped.
median_radius	A numeric(1) passed to magick::image_median. If NA this step is skipped.
negate	A logical(1) controlling whether to use magick::negate.

Details

The magick functions are used in the sequence represented by the arguments to this function. You can alternatively use this function sequentially. Or directly use the magick package.

Value

A magick image object such as the one returned by magick::image_read.

See Also

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

Examples

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

    ## Reduce brightness to 25%
    x <- img_edit(spe, sampleid = "151507", brightness = 25)
    plot(x)
}

LieberInstitute/spatialLIBD documentation built on April 21, 2024, 6:47 p.m.