Run Harmony algorithm — RunHarmony2 • scop

This is a modified version of harmony::RunHarmony specifically designed for compatibility with RunSymphonyMap.

Usage

RunHarmony2(object, ...)

# S3 method for class 'Seurat'
RunHarmony2(
  object,
  group.by.vars,
  assay = NULL,
  reduction = "pca",
  dims.use = 1:30,
  project.dim = TRUE,
  reduction.name = "Harmony",
  reduction.save = NULL,
  reduction.key = "Harmony_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

Arguments

object: A Seurat object.
...: Additional arguments to be passed to harmony::RunHarmony.
group.by.vars: The batch variable name.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
reduction: Which dimensionality reduction to use. Default is "pca".
dims.use: The dimensions to be used. Default is 1:30.
project.dim: Whether to project dimension reduction loadings. Default is TRUE.
reduction.name: The name of the reduction to be stored in the Seurat object. Default is "Harmony".
reduction.save: Deprecated alias for reduction.name, retained for compatibility with harmony::RunHarmony.Seurat.
reduction.key: The prefix for the column names of the Harmony embeddings. Default is "Harmony_".
verbose: Whether to print the message. Default is TRUE.
seed.use: Random seed for reproducibility. Default is 11.

Examples

data(panc8_sub)
panc8_sub <- standard_scop(panc8_sub)
panc8_sub <- RunHarmony2(
  panc8_sub,
  group.by.vars = "tech",
  reduction = "pca"
)

CellDimPlot(
  panc8_sub,
  group.by = c("tech", "celltype"),
  reduction = "pca"
)

CellDimPlot(
  panc8_sub,
  group.by = c("tech", "celltype"),
  reduction = "Harmony"
)

panc8_sub <- standard_scop(
  panc8_sub,
  prefix = "Harmony",
  linear_reduction = "Harmony"
)

CellDimPlot(
  panc8_sub,
  group.by = c("tech", "celltype"),
  reduction = "StandardpcaUMAP2D"
)

CellDimPlot(
  panc8_sub,
  group.by = c("tech", "celltype"),
  reduction = "HarmonyUMAP2D"
)