Get default reduction from object

Returns the default reduction for the single-cell object passed. default_reduction will check for reductions in the order below. If a reduction exists, it will be returned. If not, the function will check for the next reduction on the list. If none of the reductions in the list exist, the function will return an error.

1. UMAP

2. t-SNE

3. PCA

Usage

default_reduction(object)

# S3 method for class 'Seurat'
default_reduction(object)

# S3 method for class 'SingleCellExperiment'
default_reduction(object)

# S3 method for class 'AnnDataR6'
default_reduction(object)

Arguments

object

A single cell object. Currently, Seurat, SingleCellExpleriment, and anndata objects are supported.

Details

This is a utility function that is most useful for defining defaults in plotting functions, to reduce the number of required parameters end users need to supply. see our website for an example of usage in a function.

Methods (by class)

• default_reduction(Seurat): Seurat objects

  In Seurat objects, default_reduction is a wrapper for SeuratObject::DefaultDimReduc().

• default_reduction(SingleCellExperiment): SingleCellExperiment objects

  The search order for SingleCellExperiment objects is below. fetch_reduction will search in the order described for a reduction named exactly as described.

  1. UMAP

  2. TSNE

  3. PCA

• default_reduction(AnnDataR6): AnnDataR6 objects

  The search order for anndata objects is below. fetch_reduction will search in the order described for a reduction named exactly as described.

  1. X_umap

  2. X_tsne

  3. X_pca

Examples

# Seurat objects
default_reduction(AML_Seurat)
#> [1] "umap"

# SingleCellExperiment objects
default_reduction(AML_SCE())
#> [1] "UMAP"

# anndata objects
default_reduction(AML_h5ad())
#> [1] "X_umap"