Single-file (HDF5) Daf store.

A Daf store held in one .h5df HDF5 file, interoperable with Julia's DataAxesFormats.H5df. The file holds a daf marker dataset plus scalars/axes/vectors/matrices groups of typed HDF5 datasets. Requires the hdf5r package.

Usage

H5df(
  name = character(0),
  internal = new.env(parent = emptyenv()),
  cache = new.env(parent = emptyenv()),
  axis_version_counter = new.env(parent = emptyenv()),
  vector_version_counter = new.env(parent = emptyenv()),
  matrix_version_counter = new.env(parent = emptyenv())
)

H5dfReadOnly(
  name = character(0),
  internal = new.env(parent = emptyenv()),
  cache = new.env(parent = emptyenv()),
  axis_version_counter = new.env(parent = emptyenv()),
  vector_version_counter = new.env(parent = emptyenv()),
  matrix_version_counter = new.env(parent = emptyenv())
)

h5df(path, mode = c("r", "r+", "w", "w+"), name = NULL)

Arguments

name: Human-readable identifier. Default derived from the store's name scalar if present, else basename(path).
internal: Internal per-store environment used by format backends to stash backend-specific state; reserved for package use.
cache: Three-tier cache environment (mapped / memory / query). See new_cache_env().
axis_version_counter: Environment tracking per-axis mutation counters; invalidates cached reads when an axis is modified.
vector_version_counter: Environment tracking per-vector mutation counters.
matrix_version_counter: Environment tracking per-matrix mutation counters.
path: Path to a .h5df file.
mode: One of "r" (read; must exist), "r+" (append; must exist), "w" (create; fails if it is already a daf store), "w+" (create or append).

Value

An H5df (writable modes) or H5dfReadOnly ("r").

Examples

if (requireNamespace("hdf5r", quietly = TRUE)) {
  path <- tempfile("dafr-", fileext = ".h5df")
  d <- h5df(path, mode = "w")
  add_axis(d, "cell", c("c1", "c2"))
  set_scalar(d, "organism", "human")
  rm(d)
  unlink(path)
}