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 harmony::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 <- RunHarmony2(
panc8_sub,
group.by.vars = "tech",
reduction = "pca"
)
#> Transposing data matrix
#> Initializing state using k-means centroids initialization
#> Harmony 1/10
#> Harmony 2/10
#> Harmony 3/10
#> Harmony 4/10
#> Harmony 5/10
#> Harmony 6/10
#> Harmony 7/10
#> Harmony converged after 7 iterations
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "pca"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "Harmony"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
