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Convert a Seurat object to an AnnData object

Source: R/DataConvert.R
srt_to_adata.Rd

Convert a Seurat object to an AnnData object

Usage

srt_to_adata(
  object,
  features = NULL,
  assay_x = "RNA",
  layer_x = "counts",
  assay_y = c("spliced", "unspliced"),
  layer_y = "counts",
  reductions = NULL,
  graphs = NULL,
  neighbors = NULL,
  convert_tools = FALSE,
  convert_misc = FALSE,
  prepare_env = TRUE,
  verbose = TRUE,
  srt = NULL
)

Arguments

object

A Seurat object.

features

Optional vector of features to include in the anndata object. Default is all features in assay_x.

assay_x

Assay to convert as the main data matrix in the anndata object.

layer_x

Layer name for assay_x in the Seurat object.

assay_y

Assays, or extra layers of assay_x, to convert as layers in the anndata object. Each name is matched against the assays of the object first, then against the layers of assay_x, which covers velocity matrices such as spliced and unspliced stored as layers of a Seurat v5 RNA assay.

layer_y

Layer names for the assays in assay_y. It is ignored for names that are matched as layers of assay_x, where the layer name itself is used.

reductions

Character vector specifying which Seurat reductions to convert into obsm. Default is NULL, which converts all available reductions.

graphs

Character vector specifying which Seurat graphs to convert into obsp. Default is NULL, which converts all available graphs.

neighbors

Character vector specifying which Seurat neighbor objects to convert into obsp. Default is NULL, which converts all available neighbor objects.

convert_tools

Whether to convert the tool-specific data.

convert_misc

Whether to convert the miscellaneous data.

prepare_env

Whether to prepare and validate the Scanpy Python environment before conversion. Wrapper functions that already prepared the environment should pass FALSE to keep one reticulate binding.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A anndata object.

See also

adata_to_srt

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
adata <- srt_to_adata(pancreas_sub)
adata

# Or save as a h5ad/loom file
adata$write_h5ad(
  "pancreas_sub.h5ad"
)
adata$write_loom(
  "pancreas_sub.loom",
  write_obsm_varm = TRUE
)
} # }