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Write Zarr

Source: R/write_zarr.R
write_zarr.Rd

Write a Zarr file

Usage

write_zarr(
  object,
  path,
  compression = c("none", "gzip", "blosc", "zstd", "lzma", "bz2", "zlib", "lz4"),
  mode = c("w-", "r", "r+", "a", "w", "x"),
  ...
)

Arguments

object

The object to write, either a SingleCellExperiment::SingleCellExperiment or a SeuratObject::Seurat object

path

Path of the file to write to

compression

The compression algorithm to use when writing the Zarr file. Can be one of "none", "gzip", "blosc", "zstd", "lzma", "bz2", "zlib", "lz4". Defaults to "none". See help("compressors", package = "Rarr").

mode

The mode to open the Zarr file.

  • a creates a new file or opens an existing one for read/write

  • r+ opens an existing file for read/write

  • w creates a file, truncating any existing ones

  • w-/x are synonyms creating a file and failing if it already exists

...

Additional arguments passed to as_AnnData() or as_ZarrAnnData()

Value

path invisibly

Details

Zarr format

New stores are written in the Zarr v3 format. Pass zarr_format = 2 to write a Zarr v2 store instead, or set options(anndataR.zarr_format = 2) to change the default for the current session. However, if zarr_format = 3 is passed to write_zarr, it will override options(anndataR.zarr_format = 2). Writing to an existing store always uses the format of that store. See as_ZarrAnnData() for details.

NULL values

For compatibility with changes in Python anndata 0.12.0, NULL values in uns are written to Zarr files as a NULL dataset (instead of not being written at all). To disable this behaviour, set option(anndataR.write_null = FALSE). This may be required to allow the file to be read by older versions of Python anndata.

Examples

adata <- AnnData(
  X = matrix(1:5, 3L, 5L),
  layers = list(
    A = matrix(5:1, 3L, 5L),
    B = matrix(letters[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)
)
zarr_store <- tempfile(fileext = ".zarr")
adata$write_zarr(zarr_store)

# Write a Zarr v2 store instead of the default v3
zarr_store <- tempfile(fileext = ".zarr")
adata$write_zarr(zarr_store, zarr_format = 2)

# Write a SingleCellExperiment as a Zarr store
if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
  ncells <- 100
  counts <- matrix(rpois(20000, 5), ncol = ncells)
  logcounts <- log2(counts + 1)

  pca <- matrix(runif(ncells * 5), ncells)
  tsne <- matrix(rnorm(ncells * 2), ncells)

  sce <- SingleCellExperiment::SingleCellExperiment(
    assays = list(counts = counts, logcounts = logcounts),
    reducedDims = list(PCA = pca, tSNE = tsne)
  )

  adata <- as_AnnData(sce)
  zarr_store <- tempfile(fileext = ".zarr")
  adata$write_zarr(zarr_store)
}

# Write a Seurat as a Zarr
if (requireNamespace("Seurat", quietly = TRUE)) {
  library(Seurat)

  counts <- matrix(1:15, 5L, 3L)
  dimnames(counts) <- list(
    LETTERS[1:5],
    letters[1:3]
  )
  cell.metadata <- data.frame(
    row.names = letters[1:3],
    cell = 1:3
  )
  obj <- CreateSeuratObject(counts, meta.data = cell.metadata)
  gene.metadata <- data.frame(
    row.names = LETTERS[1:5],
    gene = 1:5
  )
  obj[["RNA"]] <- AddMetaData(GetAssay(obj), gene.metadata)

  adata <- as_AnnData(obj)
  zarr_store <- tempfile(fileext = ".zarr")
  adata$write_zarr(zarr_store)
}
#> Warning: Data is of class matrix. Coercing to dgCMatrix.