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Add border or core spot selections to SpatialExperiment colData

Source: R/R-spe.R
add_borders_to_spe.Rd

This function takes spot selection results (either border or core spots) and adds them as annotations in the colData of a SpatialExperiment object.

Usage

add_borders_to_spe(spe, border = NULL, core = NULL, erase = FALSE)

Arguments

spe

A SpatialExperiment object from which the selection dataframes were derived.

border

Optional data.frame of border spots. Can be output from either [select_border_spots()] or [build_all_borders()]. Expected columns: spot_id, interface, mode.

core

Optional data.frame of core spots. Can be output from either [select_core_spots()] or [build_all_cores()]. Expected columns: spot_id, interface, mode.

erase

Logical. If `TRUE`, erase pre-existing battlefield columns before adding new ones. If `FALSE` (default), issue a warning if columns already exist and skip adding them.

Value

The SpatialExperiment object with updated colData.

Details

At least `border` must be provided. `core` is optional. If `core` is provided without `border`, an error is raised.

The following unified columns are added: - `is_border`: logical, TRUE if spot is a border spot, FALSE or NA otherwise - `is_core`: logical, TRUE if spot is a core spot, FALSE or NA otherwise - `interface`: the target interface cluster - `border_mode`: character, "inner", "outer", or NA (from the `mode` column in input data)

Examples

data("visiumHD_16um_simulated_spe", package = "Battlefield")
spe <- visiumHD_16um_simulated_spe
#> Loading required namespace: SpatialExperiment
df <- data.frame(
  spot_id = colnames(spe),
  x = spatialCoords(spe)[, 1],
  y = spatialCoords(spe)[, 2],
  cluster = colData(spe)$cluster
)
#> Error in spatialCoords(spe): could not find function "spatialCoords"
# Using build_all_borders and build_all_cores
all_borders <- build_all_borders(df, k = 6)
#> Error in df[[cluster_col]]: object of type 'closure' is not subsettable
all_cores <- build_all_cores(df, all_borders, region = "inner")
#> Error in build_all_cores(df, all_borders, region = "inner"): unused argument (region = "inner")

# Or using individual select functions
border_3_to_4 <- select_border_spots(df, cluster = 3, interface = 4, k = 6)
#> Error in select_border_spots(df, cluster = 3, interface = 4, k = 6): all(coord_cols %in% colnames(df)) is not TRUE
core_3_to_4 <- select_core_spots(df, all_borders, cluster = 3, interface = 4)
#> Error in select_core_spots(df, all_borders, cluster = 3, interface = 4): all(coord_cols %in% colnames(df)) is not TRUE