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Convert a seurat object to an anndata object using reticulate

Source: R/srt_to_adata.R
srt_to_adata.Rd

This function takes a Seurat object and converts it to an anndata object using the reticulate package.

Usage

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

Arguments

srt

A Seurat object.

features

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

assay_x

Assay to convert as the main data matrix (X) 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.

convert_tools

Logical indicating whether to convert the tool-specific data.

convert_misc

Logical indicating whether to convert the miscellaneous data.

verbose

Logical indicating whether to print verbose messages during the conversion process.

Value

A anndata object.

Examples

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

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