Reconstruct structure from spe object with given image id

Usage

reconstructShapeDensityImage(
  spe,
  marks,
  imageCol = NULL,
  imageId = NULL,
  markSelect,
  dim = 500,
  bndw = NULL,
  thres = NULL,
  complement = FALSE
)

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
dim: numeric; x dimension of the final reconstruction. A lower resolution speed up computation but lead to less exact reconstruction. Default = 500
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.
thres: numeric; intensity threshold for the reconstruction; if NULL the threshold is set as the mean between the mode of the pixel intensity distributions
complement: logical; reconstruct everything but the mark of interest, default = FALSE

Value

sf object of class POLYGON

Examples

data("sostaSPE")
struct <- reconstructShapeDensityImage(sostaSPE,
    marks = "cellType", imageCol = "imageName", imageId = "image1",
    markSelect = "A", dim = 500
)
plot(struct)