calculate_summary_distances_of_cells_to_borders

Returns the mean, median and standard deviation of the distances between a specified cell type to the border.

Usage

calculate_summary_distances_of_cells_to_borders(
  sce_object,
  cell_types_of_interest,
  feature_colname = "Cell.Type"
)

Arguments

sce_object

SingleCellExperiment object whose metadata contains the information of tumour structure and cell distances to tumour border (has column "Region" and "Distance.To.Border").

cell_types_of_interest

String Vector of cell types to consider.

feature_colname

String specifying which column the interested cell types are from.

Value

A data.frame is returned

Examples

sce_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"

sce_dist <- calculate_distance_to_tumour_margin(sce_border)
#> [1] "Markers had been selected in pair-wise distance calculation: "
#> [1] "Non-border" "Border"    
sce_structure <- define_structure(sce_dist, names_of_immune_cells =
c("Immune1","Immune2","Immune3"), feature_colname = "Cell.Type",
n_margin_layers = 5)
calculate_summary_distances_of_cells_to_borders(sce_structure,
cell_types_of_interest = c("Immune1","Immune3"),feature_colname = "Cell.Type")
#>                    Cell.Type       Area    Min_d    Max_d    Mean_d  Median_d
#> 1 All_cell_types_of_interest Tumor_area 10.93225 192.4094  86.20042  88.23299
#> 2 All_cell_types_of_interest     Stroma 10.02387 971.5638 195.10637 101.95113
#> 3                    Immune1 Tumor_area      Inf     -Inf       NaN        NA
#> 4                    Immune1     Stroma 84.20018 970.7749 346.14096 301.01535
#> 5                    Immune3 Tumor_area 10.93225 192.4094  86.20042  88.23299
#> 6                    Immune3     Stroma 10.02387 971.5638 102.79227  68.19218
#>    St.dev_d
#> 1  45.27414
#> 2 194.68507
#> 3        NA
#> 4 187.04247
#> 5  45.27414
#> 6 131.32714