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Convert a Seurat object to an AnnData object

Source: R/Seurat.R
to_Seurat.Rd

to_Seurat() converts an AnnData object to a Seurat object. Only one assay can be converted at a time. Arguments are used to configure the conversion. If NULL, the functions to_Seurat_guess_* will be used to guess the mapping.

Usage

to_Seurat(
  adata,
  assay_name = "RNA",
  layers_mapping = NULL,
  reduction_mapping = NULL,
  graph_mapping = NULL,
  misc_mapping = NULL
)

Arguments

adata

An AnnData object to be converted

assay_name

Name of the assay to be created (default: "RNA").

layers_mapping

A named list to map AnnData layers to Seurat layers. See section "Layer mapping" for more details.

reduction_mapping

A named list to map AnnData reductions to Seurat reductions. Each item in the list must be a named list with keys 'key', 'obsm', and 'varm'. See section "Reduction mapping" for more details.

graph_mapping

A named list to map AnnData graphs to Seurat graphs. Each item in the list must be a character vector of length 1. See section "Graph mapping" for more details.

misc_mapping

A named list to map miscellaneous data to the names of the data in the Seurat object. See section "Miscellaneous mapping" for more details.

Value

A Seurat object

Layer mapping

A named list to map AnnData layers to Seurat layers. Each item in the list must be a character vector of length 1, where the values correspond to the names of the layers in the AnnData object, and the names correspond to the names of the layers in the resulting Seurat object. A value of NULL corresponds to the AnnData X slot.

Example: layers_mapping = list(counts = "counts", data = NULL, foo = "bar").

If NULL, the internal function to_Seurat_guess_layers will be used to guess the layer mapping as follows:

  • All AnnData layers are copied to Seurat layers by name.

Reduction mapping

A named list to map AnnData $obsm and $varm to Seurat reductions. Each item in the list must be a named list with keys 'key', 'obsm', and 'varm'. Example: reduction_mapping = list(pca = list(key = "PC_", obsm = "X_pca", varm = "PCs")).

If NULL, the internal function to_Seurat_guess_reductions will be used to guess the reduction mapping as follows:

  • All $obsm items starting with X_ are copied by name.

Graph mapping

A named list mapping graph names to the names of the graphs in the AnnData object. Each item in the list must be a character vector of length 1. The values correspond to the names of the graphs in the resulting Seurat object, while the names correspond to the names of the graphs in the AnnData object.

Example: graph_mapping = list(nn = "connectivities").

If NULL, the internal function to_Seurat_guess_graphs will be used to guess the graph mapping as follows:

  • An obsp named connectivities will be mapped to nn.

  • Other graphs starting with connectivities_ are stripped of the prefix and copied by name.

Miscellaneous mapping

A named list mapping miscellaneous data to the names of the data in the AnnData object. Each item in the list must be a vector with one or two elements. The first element must be one of: 'X', 'layers', 'obs', 'obsm', 'obsp', 'var', 'varm', 'varp', 'uns'. The second element is the name of the data in the corresponding slot. If the second element is not present, the whole slot as specified by the first element will be used.

Example: misc_mapping = list(uns = "uns", varp_neighbors = c("varp", "neighbors")).

If NULL, the internal function to_Seurat_guess_misc will be used to guess the miscellaneous mapping as follows:

  • If $uns is defined, all values in $uns are copied to the Seurat misc.

Examples

ad <- AnnData(
  X = matrix(1:5, 3L, 5L),
  obs = data.frame(row.names = LETTERS[1:3], cell = 1:3),
  var = data.frame(row.names = letters[1:5], gene = 1:5)
)
to_Seurat(ad)
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
#> An object of class Seurat 
#> 5 features across 3 samples within 1 assay 
#> Active assay: RNA (5 features, 0 variable features)
#>  1 layer present: counts