Intensity plot — shapeIntensityImage • sosta

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,
  imageCol,
  imageId,
  markSelect,
  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
imageCol: character; name of a column in colData that corresponds to the image
imageId: character; image id, must be present in imageCol
markSelect: character; name of mark that is to be selected for the reconstruction
bndw: numeric; smoothing bandwidth in the density estimation, corresponds to the sigma parameter in the density.ppp function, if no value is given the bandwidth 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

data("sostaSPE")
shapeIntensityImage(sostaSPE,
    marks = "cellType", imageCol = "imageName",
    imageId = "image1", markSelect = "A"
)