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.
...: Passed to harmony::RunHarmony.
group.by.vars: The batch variable name.
assay: Assay to use. NULL uses the default assay.
reduction: Linear reduction used as input.
dims.use: The dimensions to be used.
project.dim: Whether to project dimension reduction loadings.
reduction.name: Reduction to be stored in the Seurat object.
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.
verbose: Whether to print the message. Default is TRUE.
seed.use: Random seed.

Examples

data(panc8_sub)
panc8_sub <- RunStandardWorkflow(panc8_sub)
#> ℹ [2026-10-11 23:19:55] Start standard processing workflow...
#> ℹ [2026-10-11 23:19:55] Checking a list of <Seurat>...
#> ! [2026-10-11 23:19:55] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-10-11 23:19:55] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 23:19:55] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 23:19:56] Use the separate HVF from `srt_list`
#> ℹ [2026-10-11 23:19:56] Number of available HVF: 2000
#> ℹ [2026-10-11 23:19:56] Finished check
#> ℹ [2026-10-11 23:19:56] Perform `ScaleData()`
#> ℹ [2026-10-11 23:19:56] Perform pca linear dimension reduction
#> ℹ [2026-10-11 23:19:56] Use stored estimated dimensions 1:26 for Standardpca
#> ℹ [2026-10-11 23:19:57] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-10-11 23:19:57] Reorder clusters...
#> ℹ [2026-10-11 23:19:57] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-10-11 23:19:57] Perform umap nonlinear dimension reduction
#> ✔ [2026-10-11 23:20:05] Standard processing workflow completed
panc8_sub <- RunHarmony2(
  panc8_sub,
  group.by.vars = "tech",
  reduction = "pca"
)
#> Transposing data matrix
#> Using automatic lambda estimation
#> Thetas: 2
#> Initializing state using k-means centroids initialization
#> Initializing centroids
#> Harmony 1/10
#> Harmony 2/10
#> Harmony 3/10
#> Harmony 4/10
#> Harmony 5/10
#> Harmony 6/10
#> Harmony 7/10
#> Harmony 8/10
#> Harmony 9/10
#> Harmony converged after 9 iterations

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


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


panc8_sub <- RunStandardWorkflow(
  panc8_sub,
  prefix = "Harmony",
  linear_reduction = "Harmony"
)
#> ℹ [2026-10-11 23:20:55] Start standard processing workflow...
#> ℹ [2026-10-11 23:20:55] Checking a list of <Seurat>...
#> ℹ [2026-10-11 23:20:55] Data 1/1 of the `srt_list` has been log-normalized
#> ℹ [2026-10-11 23:20:55] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 23:20:56] Use the separate HVF from `srt_list`
#> ℹ [2026-10-11 23:20:56] Number of available HVF: 2000
#> ℹ [2026-10-11 23:20:56] Finished check
#> ℹ [2026-10-11 23:20:56] Perform `ScaleData()`
#> ℹ [2026-10-11 23:20:56] Perform Harmony linear dimension reduction
#> ℹ [2026-10-11 23:20:56] `linear_reduction` Harmony is already existed. Skip calculation
#> ℹ [2026-10-11 23:20:56] Use stored estimated dimensions 1:14 for HarmonyHarmony
#> ℹ [2026-10-11 23:20:56] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-10-11 23:20:56] Reorder clusters...
#> ℹ [2026-10-11 23:20:56] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-10-11 23:20:56] Perform umap nonlinear dimension reduction
#> ✔ [2026-10-11 23:21:05] Standard processing workflow completed

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


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