Set Default Dimensionality Reduction Set the default dimensionality reduction for a specific assay in a Seurat object.

Searches for DimReducs matching “umap”, “tsne”, or “pca”, case-insensitive, and in that order. Priority given to DimReducs matching the DefaultAssay or assay specified (eg. “pca” for the default assay weights higher than “umap” for a non-default assay)

DefaultDimReduc(object, ...) <- value

DefaultDimReduc(object, assay = NULL)

# S3 method for class 'Seurat'
DefaultDimReduc(object, ...) <- value

Arguments

object: A Seurat object
...: Arguments passed to other methods
value: Character string specifying the name of the dimensionality reduction to set as default. Set to NULL to clear the default for the current assay.
assay: Name of assay to use; defaults to the default assay of the object

Value

A Seurat object with the default dimensionality reduction updated.

The default DimReduc, if possible

Details

This function stores the default dimensionality reduction on a per-assay basis. This function only needs to be run if users want to override the default DimReduc selection logic that Seurat employs. When `DefaultDimReduc()` is called, it will return the assay-specific default if one has been set. If none was explicitly set then default Seurat logic will be used to select default.

Examples

DefaultDimReduc(pbmc_small)
#> [1] "tsne"

if (FALSE) { # \dontrun{
# Set UMAP as default for RNA assay
DefaultDimReduc(seurat_obj) <- "umap"

# Clear the set default
DefaultDimReduc(seurat_obj) <- NULL
} # }