calculate_cell_proportions

Source: R/calculate_cell_proportions.R

Calculate the number and proportion of each cell phenotype in an image

calculate_cell_proportions(
  sce_object,
  column = "Phenotype",
  reference_celltypes = NULL,
  celltypes_to_exclude = NULL
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce
column

Column of cells to choose the phenotype from (e.g. Phenotype, Cell.Type, etc)
reference_celltypes

Vector specifying reference phenotypes. If NULL (default), then the proportion of each cell type against all cells is returned. Alternatively, a custom vector of cell types can be used as input, and these will be used as the denominator in the calculation of the proportions.
celltypes_to_exclude

Vector specifying cell types to exclude. For example "OTHER" will exclude that celltype from the Total. If NULL, all cell types are included

Value

A data.frame is returned