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 harmony::RunHarmony.
- group.by.vars
The batch variable name.
- reduction
The reduction to be used. 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.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
The random seed to be used. Default is
11.
Examples
panc8_sub <- RunHarmony2(
panc8_sub,
group.by.vars = "tech",
reduction = "pca"
)
#> ℹ [2025-09-20 13:42:59] Installing: harmony...
#>
#> → Will install 2 packages.
#> → All 2 packages (0 B) are cached.
#> + RhpcBLASctl 0.23-42
#> + harmony 1.2.3
#>
#> ℹ No downloads are needed, 2 pkgs are cached
#> ✔ Got RhpcBLASctl 0.23-42 (x86_64-pc-linux-gnu-ubuntu-24.04) (14.56 kB)
#> ✔ Got harmony 1.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.80 MB)
#> ✔ Installed RhpcBLASctl 0.23-42 (1s)
#> ✔ Installed harmony 1.2.3 (1.1s)
#> ✔ 1 pkg + 29 deps: kept 27, added 2, dld 2 (4.81 MB) [3.3s]
#> ℹ [2025-09-20 13:43:02] harmony@1.1.0 installed successfully
#> Error in object[[reduction]]: ‘pca’ not found in this Seurat object
#>
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "pca"
)
#> Error in DefaultReduction(srt, pattern = reduction): Unable to find any reductions
CellDimPlot(
panc8_sub,
group.by = c("tech", "celltype"),
reduction = "Harmony"
)
#> Error in DefaultReduction(srt, pattern = reduction): Unable to find any reductions