Select cell types to keep or exclude in the analysis. The output of this function also includes the original image size and cell count.
select_celltypes(
spe_object,
celltypes,
feature_colname = "Phenotype",
keep = TRUE
)SpatialExperiment object in the form of the output of
format_image_to_spe.
String Vector of celltypes of keep or exclude.
String. The column that has the interested cell types. If the cells ids are used to select cells, use "Cell.ID" for this arg.
Boolean. TRUE if vector of `celltypes` are the cells that are going to be kept, FALSE if they are to be removed.
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.
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
#> [1] 4951
attr(data_subset, "range_of_coords")
#> xmin xmax ymin ymax
#> 0.1869877 1999.9512939 0.3243161 1998.9921875
dim(data_subset)[2] # this is the new image cell number
#> [1] 819