img_edit: Edit a background image

View source: R/img_edit.R

img_editR Documentation

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

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.

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 Nov. 4, 2024, 11:57 a.m.