Run Harmony — harmony_sc • bixverse

A version of Harmony by Korsunsky et al., implemented in Rust. Performs batch correction on PCA embeddings and stores the result as a "harmony" embedding in the object.

Usage

harmony_sc(
  object,
  batch_column,
  additional_batch_columns = NULL,
  modality = c("rna", "adt"),
  harmony_params = params_sc_harmony(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object: SingleCells or SingleCellsSubset class.
batch_column: String. Column name in the object containing the primary batch labels.
additional_batch_columns: Optional character vector. Additional batch columns to regress out. If NULL, only the primary batch column is used.
modality: String. One of c("rna", "adt"). You can only use "adt" on SingleCellsMultiModal class.
harmony_params: List. Output of params_sc_harmony().
seed: Integer. For reproducibility.
.verbose: Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

The object with a "harmony" embedding added. If no PCA embeddings are found, returns the object unchanged with a warning.

Examples

# Harmony correction of the PCA embedding
sc <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 600L, n_genes = 50L, n_batches = 3L
  )
)
sc <- harmony_sc(sc, batch_column = "batch_index", .verbose = FALSE)
dim(get_embedding(sc, "harmony"))
#> [1] 600  10

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