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Fetch reduction coordinates from single-cell objects

fetch_reduction.Rd

Returns the reduction coordinates matching the name and dimensions supplied.

Usage

fetch_reduction(object, reduction, cells = NULL, dims = c(1, 2))

# S3 method for class 'Seurat'
fetch_reduction(object, reduction, cells = NULL, dims = c(1, 2))

# S3 method for class 'SingleCellExperiment'
fetch_reduction(object, reduction, cells = NULL, dims = c(1, 2))

# S3 method for class 'AnnDataR6'
fetch_reduction(object, reduction, cells = NULL, dims = c(1, 2))

Arguments

object

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

reduction

the name of the reduction to pull coordinates from.

cells

cell IDs for which to pull reduction data. If NULL, coordinates will be returned from all cells in the object. Cell IDs can be generated with fetch_cells().

dims

a numeric vector indicating the dimensions to pull. Currently, only two dimensions are supported, but fetch_data() supports more than two dimensions. For instructions on pulling more than two dimensions at once, see the examples of fetch_data().

Details

See our GitHub.io website for additional information and examples.

Methods (by class)

  • fetch_reduction(Seurat): Seurat objects

  • fetch_reduction(SingleCellExperiment): SingleCellExperiment objects

  • fetch_reduction(AnnDataR6): AnnDataR6 objects

Examples

# Return the first and second dimensions from the UMAP reduction
fetch_reduction(
  AML_Seurat,
  reduction = "umap",
  dims = c(1, 2)
  ) |> str()
#> 'data.frame':	250 obs. of  2 variables:
#>  $ UMAP_1: num  -1.64 -1.5 -1.45 -1.38 -1.41 ...
#>  $ UMAP_2: num  9.9 10.13 10.21 10.51 3.39 ...