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Write H5AD

Source: R/write_h5ad.R
write_h5ad.Rd

Write an H5AD file

Usage

write_h5ad(
  object,
  path,
  compression = c("none", "gzip", "lzf"),
  chunk_size = "auto",
  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 HDF5 file. Can be one of "none", "gzip" or "lzf". Defaults to "none".

chunk_size

The target chunk size in bytes to use when writing HDF5 datasets. When "auto" (default), the chunk size is determined automatically using an algorithm that mimics h5py's auto-chunking behaviour. Set to NULL to disable chunking (contiguous storage, the rhdf5 default), or a number to use a specific target size in bytes. This only affects array-like datasets; scalar values are unaffected.

mode

The mode to open the HDF5 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()

Value

path invisibly

Details

Compression

Compression is currently not supported for Boolean arrays, they will be written uncompressed.

NULL values

For compatibility with changes in Python anndata 0.12.0, NULL values in uns are written to H5AD 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)
)
h5ad_file <- tempfile(fileext = ".h5ad")
adata$write_h5ad(h5ad_file)

# Write a SingleCellExperiment as an H5AD
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)
  h5ad_file <- tempfile(fileext = ".h5ad")
  adata$write_h5ad(h5ad_file)
}

# Write a Seurat as a H5AD
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)
  h5ad_file <- tempfile(fileext = ".h5ad")
  adata$write_h5ad(h5ad_file)
}
#> Warning: Data is of class matrix. Coercing to dgCMatrix.