This function takes layer classification results (border, intermediate, core) and adds them as annotations in the colData of a SpatialExperiment object.
Arguments
- spe
A SpatialExperiment object from which the layer dataframes were derived.
- layer
A data.frame of layer classifications. Can be output from either [create_cluster_layers()] or [create_all_layers()]. Expected columns: spot_id, layer.
- erase
Logical. If `TRUE`, erase pre-existing layer columns before adding new ones. If `FALSE` (default), issue a warning if columns already exist and skip adding them.
Details
The `layer` parameter must be provided and contain at least one row.
The following column is added: - `layer`: character, one of "border", "intermediate", "core", or NA
Examples
data("visiumHD_16um_simulated_spe", package = "Battlefield")
spe <- visiumHD_16um_simulated_spe
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"
# Or for a single cluster
cluster_1_layers <- create_cluster_layers(df, target_cluster = 1, k = 6)
#> Error in create_cluster_layers(df, target_cluster = 1, k = 6): all(coord_cols %in% colnames(df)) is not TRUE
spe <- add_layers_to_spe(spe, layer = cluster_1_layers)
#> Error: object 'cluster_1_layers' not found