identify_bordering_cells

Source: R/identify_bordering_cells2.R

Identify the cells bordering a group of cells of a particular phenotype

identify_bordering_cells2(
  sce_object,
  reference_cell,
  draw = F,
  n_of_polygons = 1,
  ahull_alpha = NULL,
  column = "Cell.Type"
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce
reference_cell

Cells positive for this marker will be used as reference
draw

Boolean if user chooses to draw the tumour area or not. Default is False.
n_of_polygons

Number specifying the number of tumour regions defined by user
ahull_alpha

Number specifying the ahull parameter. Larger number, more points included in the ahull.
column

Column to select for phenotypes. Can be Phenotypes, Cell.Type, etc