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Run Harmony v2

harmony_v2_sc.Rd

A version of Harmony v2 by Patikas et al., 2026, implemented in Rust. Performs batch correction on PCA embeddings and stores the result as a "harmony_v2" embedding in the object.

Usage

harmony_v2_sc(
  object,
  batch_column,
  additional_batch_columns = NULL,
  modality = c("rna", "adt"),
  harmony_params = params_sc_harmony_v2(),
  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_v2().

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_v2" embedding added. If no PCA embeddings are found, returns the object unchanged with a warning.

Examples

# the reimplemented Harmony, writing its own embedding
sc <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 600L, n_genes = 50L, n_batches = 3L
  )
)
sc <- harmony_v2_sc(
  sc,
  batch_column = "batch_index",
  .verbose = FALSE
)
dim(get_embedding(sc, "harmony_v2"))
#> [1] 600  10

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