After identifying the bordering cells of tissue regions and calculating the distances of each cell to the bordering cells, this function further identifies the cells that are located in the inside and outside of the identified regions, and in the internal and external margins. It also identifies particular types of cells that are infiltrated, stromal, internal margin or external margin cells.
define_structure(
spe_object,
cell_types_of_interest,
feature_colname = "Cell.Type",
n_margin_layers = 5,
margin_dist = NULL
)Arguments
- spe_object
SpatialExperiment object that contains information of tumour bordering cells and cell distances to border (`colData()` has `Region` and `Distance.To.Border` columns).
- cell_types_of_interest
String Vector of the names of the particular types of cells.
- feature_colname
String Specifying the column that contains the names of the immune cells.
- n_margin_layers
Integer. The number of layers of cells that compose the internal/external margins. Default is 5.
- margin_dist
Numeric. The width of the internal/external margins. Default is NULL. Only use when `n_margin_layers` is NULL.
Value
A new spe object is returned. Under the `Region` column, there will be potential categories including `Border` - the bordering cells, `Infiltrated.CoI` - cells of interest that present inside of the tissue regions, `Inside` - cells within the regiona excluding the `Infiltrated.CoI` cells and the cells at internal margin, `Stromal.CoI` - cells of interest that present outside of the tissue regions, `Outside` - cells outside of the tissue regions excluding the `Stromal.CoI` cells, `Internal.margin.CoI` - cells of interest that are in the internal margin of the tissue regions, `Internal.margin` - cells in the internal margin of the tissue regions excluding the `Internal.margin.CoI` cells, `External.margin.CoI` - cells of interest that are in the external margin of the tissue regions, `External.margin` - cells in the external margin of the tissue regions excluding the `External.margin.CoI` cells.
Examples
spe_border <- identify_bordering_cells(SPIAT::defined_image,
reference_cell = "Tumour", feature_colname = "Cell.Type", n_to_exclude = 10)
#> [1] "The alpha of Polygon is: 63.24375"
spe_dist <- calculate_distance_to_margin(spe_border)
#> [1] "Markers had been selected in minimum distance calculation: "
#> [1] "Non-border" "Border"
spe_structure <- define_structure(spe_dist,
cell_types_of_interest = c("Immune1","Immune2","Immune3"),
feature_colname = "Cell.Type", n_margin_layers = 5)
plot_cell_categories(spe_structure, feature_colname = "Structure")
