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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(
  srt,
  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
)

Arguments

srt

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 to convert as layers in the anndata object.

layer_y

Layer names for the assay_y in the Seurat object.

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. Set to FALSE when a wrapper already prepared the environment and reticulate must keep the same binding.

verbose

Whether to print the message. Default is TRUE.

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
)
} # }