define_celltypes: define_celltypes

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

define_celltypes

Description

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.

Usage

define_celltypes(
  spe_object,
  categories = NULL,
  category_colname = "Phenotype",
  names = NULL,
  new_colname = "Cell.Type",
  print_names = FALSE
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
categories	Vector. Names of the old cell types to be defined; if NULL, the function will use predefined categories and names
category_colname	(Phenotype) String specifying the name of the column having the categories to be defined, by default "Phenotype".
names	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'.
new_colname	(Optional) String specifying the name of the column to be added, by default "Cell.Type".
print_names	(Optional) Boolean if the user wants the original and new names printed. Default is FALSE.

Details

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.

Value

An new SPE object is returned

Examples

# 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)

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.