Write H5AD

Write an H5AD file

Usage

write_h5ad(
  object,
  path,
  compression = c("none", "gzip", "lzf"),
  mode = c("w-", "r", "r+", "a", "w", "x")
)

Arguments

object

The object to write, either a "SingleCellExperiment" or a "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".

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.

Value

path invisibly

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)
#> [1] "/tmp/Rtmp3F3EQq/file1d141f31b1b9.h5ad"

# 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 <- from_SingleCellExperiment(sce)
  h5ad_file <- tempfile(fileext = ".h5ad")
  adata$write_h5ad(h5ad_file)
}
#> [1] "/tmp/Rtmp3F3EQq/file1d1439ff2fe5.h5ad"

# 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 <- from_Seurat(obj)
  h5ad_file <- tempfile(fileext = ".h5ad")
  adata$write_h5ad(h5ad_file)
}
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
#> [1] "/tmp/Rtmp3F3EQq/file1d146d603d7d.h5ad"