Add labels to a Symphony reference post-hoc — add_symphony

Reads one or more obs columns from a SingleCells object and stores them in the reference's labels slot for use by transfer_labels_symphony(). The provided sc_object must have cells_to_keep matching the cells used at reference-build time; this is enforced by a length check against nrow(z_corr).

Usage

add_symphony_labels(reference, sc_object, columns, overwrite = FALSE)

Arguments

reference: SymphonyReference.
sc_object: SingleCells to read labels from. Typically the same object passed to build_symphony_ref().
columns: Character vector of obs column names.
overwrite: Boolean. If TRUE, existing label columns of the same name are replaced; otherwise an error is raised on collision.

Value

The reference with updated labels.

Examples

# attach obs labels to a reference built without them
ref <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 500L,
    n_genes = 50L,
    n_batches = 2L
  )
)
symphony_ref <- build_symphony_ref(
  ref,
  batch_column = "batch_index",
  hvg = get_hvg(ref) + 1L,
  harmony_params = params_sc_harmony(k = 10L),
  no_pcs = 10L,
  .verbose = FALSE
)
symphony_ref <- add_symphony_labels(
  symphony_ref,
  sc_object = ref,
  columns = "cell_grp"
)
head(get_symphony_labels(symphony_ref))
#>       cell_grp
#>         <char>
#> 1: cell_type_1
#> 2: cell_type_2
#> 3: cell_type_3
#> 4: cell_type_1
#> 5: cell_type_2
#> 6: cell_type_3

unlink(ref@dir_data, recursive = TRUE, force = TRUE)