RunHarmony2: Run Harmony algorithm

In zh542370159/SCP: Single Cell Pipeline

Run Harmony algorithm

Description

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,
  reduction = "pca",
  dims.use = 1:30,
  project.dim = TRUE,
  reduction.name = "Harmony",
  reduction.key = "Harmony_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

Arguments

object	A Seurat object.
...	Additional arguments to be passed to the RunHarmony function.
group.by.vars	A character vector specifying the batch variable name.
reduction	A character string specifying the reduction to be used. Default is "pca".
dims.use	An integer vector specifying the dimensions to be used. Default is 1:30.
project.dim	A logical value indicating whether to project dimension reduction loadings. Default is TRUE.
reduction.name	A character string specifying the name of the reduction to be stored in the Seurat object. Default is "Harmony".
reduction.key	A character string specifying the prefix for the column names of the Harmony embeddings. Default is "Harmony_".
verbose	A logical value indicating whether to print verbose output. Default is TRUE.
seed.use	An integer specifying the random seed to be used. Default is 11.

Examples

panc8_sub <- Standard_SCP(panc8_sub)
panc8_sub <- RunHarmony2(panc8_sub, group.by.vars = "tech", reduction = "Standardpca")
CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = "Standardpca")
CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = "Harmony")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.