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Save a Seurat object as an AnnData Zarr store

Source: R/SaveZarr.R
writeZarr.Rd

Writes a Seurat object to AnnData Zarr v2 format (.zarr directory). The output is readable by Python anndata.read_zarr(), scanpy, and any tool supporting the AnnData on-disk specification.

Usage

writeZarr(
  object,
  filename,
  assay = DefaultAssay(object),
  overwrite = FALSE,
  compressor = NULL,
  compression_level = NULL,
  verbose = TRUE,
  ...
)

Arguments

object

A Seurat object

filename

Path for the output .zarr directory

assay

Name of assay to export (default: DefaultAssay(object))

overwrite

If TRUE, overwrite existing zarr store

compressor

Compression codec. NULL (default) auto-selects: Zstd when a Zstd codec package is on the search path, otherwise zlib. As of 2026 there is no maintained CRAN Zstd-bytes wrapper for R, so the default falls through to zlib for most users; install zstdlite from source to enable Zstd. Other accepted values: "zstd", "zlib"/"gzip", "blosc" (requires the blosc package), "none", or a list list(id = ..., level = ...) matching the Zarr v2 compressor schema. Zstd at level 3 typically gives 1.5–2x smaller files than zlib level 6 and decompresses 3–5x faster.

compression_level

Override the per-codec default level. NULL uses zstd 3, zlib GetCompressionLevel(), blosc 5.

verbose

Show progress messages

...

Additional arguments (currently unused)

Value

Invisibly returns filename