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AnnData interop

Source: vignettes/anndata.Rmd
anndata.Rmd

DafAnnData facade

If you’ve been using anndata / scanpy / Seurat, the facade exposes a Daf with familiar property names:

d <- example_cells_daf()
ann <- as_anndata(d)
ann$n_obs
#> [1] 856
ann$n_vars
#> [1] 683
head(ann$obs_names)
#> [1] "demux_07_12_20_1_AACAAGATCCATTTCA-1" "demux_07_12_20_1_AACGAAAGTCCAATCA-1"
#> [3] "demux_07_12_20_1_AAGACAAAGTTCCGTA-1" "demux_07_12_20_1_AGACTCATCTATTGTC-1"
#> [5] "demux_07_12_20_1_AGATAGACATTCCTCG-1" "demux_07_12_20_1_ATCGTAGTCCAGTGCG-1"
dim(ann$X)
#> [1] 856 683

The facade is read-only: ann$X <- ... errors. To modify data, write to the underlying Daf: set_matrix(d, ...).

Loading h5ad 

d <- h5ad_as_daf("path/to/file.h5ad")

Requires hdf5r (a Suggests dep): install.packages("hdf5r").

Writing h5ad 

daf_as_h5ad(d, "out.h5ad", overwrite = TRUE)

Fixture round-trip 

fixture <- system.file("extdata", "small_test.h5ad", package = "dafr")
if (file.exists(fixture) && requireNamespace("hdf5r", quietly = TRUE)) {
    d <- h5ad_as_daf(fixture)
    cat("loaded:", daf_name(d), "\n")
    cat("n_obs:", length(axis_entries(d, "obs")), "\n")
    cat("n_vars:", length(axis_entries(d, "var")), "\n")
}
#> loaded: small_test 
#> n_obs: 50 
#> n_vars: 20

What the h5ad readers translate

h5ad_as_daf() (and daf_as_h5ad() in the other direction) cover:

  • /X dense and sparse (csr_matrix, csc_matrix) - sparse is round-tripped via Matrix::sparseMatrix.
  • /obs and /var columns: plain datasets and categorical groups (read as factor, ordered or not).
  • /layers - dense layers become extra obs x var matrices keyed by the layer name.
  • /obsm and /varm dense matrices - each is placed on a synthetic axis named obsm_<name>_dim / varm_<name>_dim.
  • /uns scalars (flat and nested; nested keys are flattened with _).

Things still NOT translated (escalated via unsupported_handler, default WARN_HANDLER, then skipped):

  • /obsp and /varp (square per-pair matrices on obs/var).
  • /raw (the legacy raw counts slot).
  • Sparse layers / obsm / varm entries; only dense forms are read.
  • Group-valued obs/var columns other than categorical.

If a strict round-trip matters, pass unsupported_handler = ERROR_HANDLER so unhandled entries hard-fail instead of being dropped silently.