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From names of reduction keys for fetch_data

reduction_dimnames.Rd

Given the name of a reduction and a set of dimensions, this function will return the names of each dimension as it appears in the reduction matrix. The output of this function can be passed to the vars parameter of fetch_data() to facilitate the specification of reduction coordinates to return from this function.

Usage

reduction_dimnames(object, reduction, dims)

# S3 method for class 'Seurat'
reduction_dimnames(object, reduction, dims)

# S3 method for class 'SingleCellExperiment'
reduction_dimnames(object, reduction, dims)

# S3 method for class 'AnnDataR6'
reduction_dimnames(object, reduction, dims)

Arguments

object

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

reduction

the name of the reduction.

dims

a numeric vector with the dimensions for which names should be returned.

Methods (by class)

  • reduction_dimnames(Seurat): Seurat objects

  • reduction_dimnames(SingleCellExperiment): SingleCellExperiment objects

  • reduction_dimnames(AnnDataR6): AnnDataR6 objects

Examples

# From names for first and second UMAP dimensions and 
# pass to fetch_data
dimnames <- reduction_dimnames(
  AML_Seurat,
  reduction = "umap",
  dims = c(1, 2)
  )
  
dimnames
#> [1] "UMAP_1" "UMAP_2"

fetch_data(
  AML_Seurat,
  vars = dimnames
  ) |> 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 ...
  
  
# Form names for first five PCA dimensions and 
# pass to fetch_data
dimnames <- reduction_dimnames(
  AML_Seurat,
  reduction = "pca",
  dims = c(1:5)
  )
  
dimnames
#> [1] "PC_1" "PC_2" "PC_3" "PC_4" "PC_5"

fetch_data(
  AML_Seurat,
  vars = dimnames
  ) |> str()
#> 'data.frame':	250 obs. of  5 variables:
#>  $ PC_1: num  3.91 3.67 2.97 2.88 42.94 ...
#>  $ PC_2: num  1.676 -0.157 0.716 1.103 -11.258 ...
#>  $ PC_3: num  1.86 3.03 2.6 3.68 -4 ...
#>  $ PC_4: num  1.308 0.649 -0.415 0.734 25.255 ...
#>  $ PC_5: num  -1.09 -2.1 -1.68 -1.16 8.28 ...