Aggregate Deconvolution Results — aggregate

Aggregates deconvolution results by merging result columns in the spatial object. This function now supports aggregating multiple cell types by passing a list of cell types. The older method of specifying two separate cell types is deprecated but still supported for backward compatibility.

Usage

aggregate_results(
  spatial_obj = NULL,
  cell_types = NULL,
  cell_type_1 = NULL,
  cell_type_2 = NULL,
  name = NULL,
  remove = FALSE
)

Arguments

spatial_obj: SpatialExperiment containing deconvolution results.
cell_types: A list of cell types to aggregate. This is the preferred method for specifying cell types to aggregate. If this parameter is used, 'cell_type_1' and 'cell_type_2' are ignored.
cell_type_1: (Deprecated) The first cell type to aggregate, included for backward compatibility. Use 'cell_types' for new code.
cell_type_2: (Deprecated) The second cell type to aggregate, included for backward compatibility. Use 'cell_types' for new code.
name: Optional new name for the aggregated result. If not provided, a name is generated automatically by concatenating the cell type names.
remove: Logical, specifies whether to remove the provided cell types from the spatial object after aggregation.

Value

A SpatialExperiment object containing the aggregation of the provided cell types.

Details

The function will aggregate the specified cell types by summing their corresponding columns in the spatial object. If the deprecated parameters 'cell_type_1' and 'cell_type_2' are used, a warning is issued, and these types are added to the 'cell_types' list for aggregation.

Examples

if (FALSE) {
# For new code, use:
aggregate_results(spatial_data_3, cell_types = c("cell_type_A", "cell_type_B"))

# For backward compatibility:
aggregate_results(spatial_data_3, cell_type_1 = "cell_type_A", cell_type_2 = "cell_type_B")
}