Plot distribution of image intensity values

Plot distribution of intensity values using either a density plot or a histogram. Useful for finding image artefact outliers and determining reasonable scaling cutoffs.

Usage

distGiottoImage(
  gobject = NULL,
  image_type = "largeImage",
  image_name = NULL,
  giottoLargeImage = NULL,
  method = c("dens", "hist"),
  show_max = TRUE,
  ...
)

Arguments

gobject

giotto object

image_type

image object type (only supports largeImage and is set as default)

image_name

name of image object to use

giottoLargeImage

giotto large image object

method

plot type to show image intensity distribution

show_max

logical. Plot the set max intensity as a vertical red line

...

additional params to pass to terra::hist() or terra::density()

Value

density or histogram plot

Details

Plot is generated from a downsampling of the original image

Plotting method 'dens'

Density plot of intensity values for image objects. N total values examined. Bandwidth refers to the curve smoothing value applied.

Plotting method 'hist'

Histogram of intensity values for image objects.

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

distGiottoImage(g, image_name = "image")