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Intensity plot

Source: R/reconstructShapePPP.R
shapeIntensityImage.Rd

This function plots the intensity of a point pattern image and displays a histogram of the intensity values. Note that intensities less than largest intensity value divided by 250 are not displayed in the histogram.

Usage

shapeIntensityImage(
  spe,
  marks,
  image_col,
  image_id,
  mark_select,
  bndw = NULL,
  dim = 500
)

Arguments

spe

SpatialExperiment; a object of class SpatialExperiment

marks

character; name of column in colData that will correspond to the ppp marks

image_col

character; name of a column in colData that corresponds to the image

image_id

character; image id, must be present in image_col

mark_select

character; name of mark that is to be selected for the reconstruction

bndw

numeric; bandwith of the sigma parameter in the density estimation, if no value is given the bandwith is estimated using cross validation with the bw.diggle function.

dim

numeric; x dimension of the final reconstruction. A lower resolution speeds up computation but lead to less exact reconstruction. Default = 500

Value

ggplot object with intensity image and histogram

Examples

spe <- imcdatasets::Damond_2019_Pancreas("spe", full_dataset = FALSE)
#> see ?imcdatasets and browseVignettes('imcdatasets') for documentation
#> loading from cache
shapeIntensityImage(spe,
    marks = "cell_category", image_col = "image_name",
    image_id = "E04", mark_select = "islet"
)