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,
  harmony_params = params_sc_harmony(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object: SingleCells 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.
harmony_params: List. Output of params_sc_harmony().
seed: Integer. For reproducibility.
.verbose: Boolean. Controls verbosity.

Value

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