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Plotting utility function to return all cell IDs

get_all_cells.Rd

Returns a character vector with all cell names in the object. This is a utility function used to set defaults for plotting functions created by SCUBA

Usage

get_all_cells(object)

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

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

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

Arguments

object

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

Details

For additional information, see our GitHub.io website ("User Guide" article, "Data Visualization" section)

Methods (by class)

  • get_all_cells(Seurat): Seurat objects

  • get_all_cells(SingleCellExperiment): SingleCellExperiment objects

  • get_all_cells(AnnDataR6): SingleCellExperiment objects

Examples

get_all_cells(AML_Seurat) |> str()
#>  chr [1:250] "487013_1" "39207_1" "861619_1" "561110_1" "283967_1" ...