Reconstruct structure from spe object with given image id

Usage

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

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
dim: numeric; x dimension of the final reconstruction. A lower resolution speed up computation but lead to less exact reconstruction. Default = 500
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.
thres: numeric; intensity threshold for the reconstruction

Value

sf object of class POLYGON

Examples

spe <- imcdatasets::Damond_2019_Pancreas("spe", full_dataset = FALSE)
#> see ?imcdatasets and browseVignettes('imcdatasets') for documentation
#> loading from cache
islet_poly <- reconstructShapeDensityImage(spe,
    marks = "cell_category",
    image_col = "image_name", image_id = "E04", mark_select = "islet", dim = 500
)
plot(islet_poly)