select_celltypes: select_celltypes

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

select_celltypes

Description

Select cell types to keep or exclude in the analysis. The output of this function also includes the original image size and cell count.

Usage

select_celltypes(
  spe_object,
  celltypes,
  feature_colname = "Phenotype",
  keep = TRUE
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
celltypes	String Vector of celltypes of keep or exclude.
feature_colname	String. The column that has the interested cell types. If the cells ids are used to select cells, use "Cell.ID" for this arg.
keep	Boolean. TRUE if vector of 'celltypes' are the cells that are going to be kept, FALSE if they are to be removed.

Value

A SpatialExperiment object is returned. The original image size and cell count can be accessed by 'attr(slim_spe, "original_cell_number")' and 'attr(slim_spe, "range_of_coords")', where 'slim_spe' is the output of this function.

Examples

data_subset <- select_celltypes(SPIAT::simulated_image,
celltypes = c("Tumour_marker","Immune_marker1","Immune_marker2",
"Immune_marker3","Immune_marker4"),
feature_colname = "Phenotype", keep=TRUE)
attr(data_subset, "original_cell_number") #cell number in the original image
attr(data_subset, "range_of_coords")
dim(data_subset)[2] # this is the new image cell number

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