Define new cell types based on the existing cell types (categories) under a selected column (e.g. base on marker combinations under "Phenotype" column). This function will create a new column to store the new cell types.
define_celltypes(
spe_object,
categories = NULL,
category_colname = "Phenotype",
names = NULL,
new_colname = "Cell.Type",
print_names = FALSE
)SpatialExperiment object in the form of the output of
format_image_to_spe.
Vector. Names of the old cell types to be defined; if NULL, the function will use predefined categories and names
(Phenotype) String specifying the name of the column having the categories to be defined, by default "Phenotype".
Vector of new names assigned to the selected categories; if NULL, the function will use predefined categories and names. Should be of the same length of `categories`.
(Optional) String specifying the name of the column to be added, by default "Cell.Type".
(Optional) Boolean if the user wants the original and new names printed. Default is FALSE.
An new SPE object is returned
Users need to specify the names of the old cell categories and under which column the old cell categories exist. Then the users specify the names of the new cell types and the name of the new column to store the new cell types. Any cell categories that are not specified in `categories` arg but present in the image will be defined as "Undefined" in the new column.
# the selected column is:
category_colname = "Phenotype"
# define the following marker combinations:
categories <- c("Tumour_marker", "Immune_marker1,Immune_marker2",
"Immune_marker1,Immune_marker3",
"Immune_marker1,Immune_marker2,Immune_marker4", "OTHER")
# the new defined cell names:
names = c("Tumour", "Immune1", "Immune2","Immune3", "Others")
# the new names are stored under this column:
new_colname <- "Cell.Type"
defined_spe <- define_celltypes(SPIAT::simulated_image,
categories = categories, category_colname = category_colname, names = names,
new_colname = new_colname)