Write a Daf to a Muon-style h5ad file.

Inverse of h5ad_as_daf(). Writes /X (dense or CSC-sparse), per-axis column groups /obs and /var (each with an _index; factor vectors emitted as h5ad categorical groups), /layers for additional matrices, and flat /uns scalars.

Usage

daf_as_h5ad(
  daf,
  path,
  obs_axis = NULL,
  var_axis = NULL,
  x_name = "UMIs",
  overwrite = FALSE,
  unsupported_handler = WARN_HANDLER
)

Arguments

daf: A DafReader.
path: Destination .h5ad path.
obs_axis: Axis name mapped to /obs. If NULL, auto-detected from "cell", "metacell".
var_axis: Axis name mapped to /var. If NULL, auto-detected from "gene".
x_name: Matrix name (on the obs_axis, var_axis pair) written as /X. Default "UMIs".
overwrite: If FALSE (default), error when path already exists; if TRUE, silently replace.
unsupported_handler: Handler for Daf features we cannot represent in h5ad. See inefficient_action_handler().

Value

Invisibly, path.

Details

Note: the write side always emits /uns flat. On read we flatten nested uns groups with a _ separator, so a round-trip of a nested uns file produces flat dotted keys on the resulting Daf.

Requires the hdf5r and Matrix packages.

Examples

if (FALSE) { # \dontrun{
d <- memory_daf()
add_axis(d, "cell", c("c1", "c2"))
add_axis(d, "gene", c("g1", "g2"))
set_matrix(d, "cell", "gene", "UMIs", matrix(1:4, 2, 2))
p <- tempfile(fileext = ".h5ad")
daf_as_h5ad(d, p, obs_axis = "cell", var_axis = "gene")
} # }