define_celltypes

Source: R/define_celltypes.R

Define celltypes of selected phenotypes. If the specified phenotype vector is shorter than the phenotypes in the sce_object, then the unspecified phenotypes will be defined as "Undefined"

define_celltypes(
  sce_object,
  phenotypes = NULL,
  names = NULL,
  column.name = "Cell.Type"
)

Arguments

sce_object

SingleCellExperiment object generated by format_image_to_sce
phenotypes

Vector of phenotypes of keep or exclude; if NULL, the function will use predefined phenotypes and names
names

Vector of new names assigned to the selected phenotypes; if NULL, the function will use predefined phenotypes and names
column.name

(Optional) String specifying the name of the column to be added, by default "Cell.Type"