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Return the default layer

default_layer.Rd

Returns the default layer for the object passed. The default layer is chosen based on the conventions used in each object to name the normalized counts layer.

Usage

default_layer(object)

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

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

# S3 method for class 'AnnDataR6'
default_layer(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_layer(Seurat): Seurat objects

    For Seurat objects, the default layer is "data".

  • default_layer(SingleCellExperiment): SingleCellExperiment objects

    For SingleCellExperiment objects, the default layer is "logcounts".

  • default_layer(AnnDataR6): Anndata objects

    For Anndata objects, the default layer is NULL, which will direct FetchData to pull feature epxression data from the X matrix.

Examples

# Seurat objects
default_layer(AML_Seurat)
#> [1] "data"

# SingleCellExperiment objects
default_layer(AML_SCE())
#> [1] "logcounts"

# anndata objects
default_layer(AML_h5ad())
#> NULL