bioalpha.h5ad_map.H5ADMap

class bioalpha.h5ad_map.H5ADMap(filename: Path, filemode: str = 'r+', raw_file: H5ADMapFile | None = None, is_raw_file: bool = True)

An AnnData mapped to a HDF5 file with limited operations.

Slicing, transpose, deletion on H5ADMap along any axis is not permitted.

Attibutes operations:

X, layers:

SparseDataset and h5py.Dataset updates are supported. Deletion and re-assignment are not supported.

obs, var, uns:

The attributes are loaded into memory. To commit changes to h5ad file, call flush().

obsm, obsp, varm, varp:

Read, write, update, deletion are fully supported.

raw: X, var, varm:

Same as H5ADMap.

Methods

chunk_X([select, replace])	Return a chunk of the data matrix X with random or specified indices.
chunked_X([axis, shuffle, chunk_size, ...])	Return an iterator over the rows of the data matrix X.
concatenate(*args, **kwargs)	Concatenate along the observations axis.
copy(filename)	Full copy, optionally on disk.
diet_subset(subset_path[, X, keys, ...])	Subset an anndata with list of keys request.
flush(*args, **kwargs)
free_temp_processing()
obs_keys()	List keys of observation annotation obs.
obs_names_make_unique([join])	Makes the index unique by appending a number string to each duplicate index element: '1', '2', etc.
obs_vector(k, *[, layer])	Convenience function for returning a 1 dimensional ndarray of values from X, layers[k], or obs.
obsm_keys()	List keys of observation annotation obsm.
rename_categories(key, categories)	Rename categories of annotation key in obs, var, and uns.
set_backed(group, key, value, *args, **kwargs)
strings_to_categoricals([df])	Transform string annotations to categoricals.
to_df([layer])	Generate shallow DataFrame.
to_memory()	Return a new AnnData object with all backed arrays loaded into memory.
transpose()	Transpose whole object.
uns_keys()	List keys of unstructured annotation.
var_keys()	List keys of variable annotation var.
var_names_make_unique([join])	Makes the index unique by appending a number string to each duplicate index element: '1', '2', etc.
var_vector(k, *[, layer])	Convenience function for returning a 1 dimensional ndarray of values from X, layers[k], or obs.
varm_keys()	List keys of variable annotation varm.
write([filename, compression, ...])	Write .h5ad-formatted hdf5 file.
write_csvs(*args, **kwargs)	Write annotation to .csv files.
write_h5ad(filename)	Write .h5ad-formatted hdf5 file.
write_loom(*args, **kwargs)	Write .loom-formatted hdf5 file.
write_zarr(*args, **kwargs)	Write a hierarchical Zarr array store.

Attributes

T	Transpose whole object.
X	Data matrix of shape n_obs × n_vars.
file
filemode
filename	Change to backing mode by setting the filename of a .h5ad file.
is_view	H5ADMap is not supported view
isbacked	True if object is backed on disk, False otherwise.
layers	Dictionary-like object with values of the same dimensions as X.
n_obs	Number of observations.
n_vars	Number of variables/features.
obs	One-dimensional annotation of observations (pd.DataFrame).
obs_names	Names of observations (alias for .obs.index).
obsm	Multi-dimensional annotation of observations (mutable structured ndarray).
obsp	Pairwise annotation of observations, a mutable mapping with array-like values.
raw	Store raw version of X and var as .raw.X and .raw.var.
shape	Shape of data matrix (n_obs, n_vars).
uns	Unstructured annotation (ordered dictionary).
var	One-dimensional annotation of variables/ features (pd.DataFrame).
var_names	Names of variables (alias for .var.index).
varm	Multi-dimensional annotation of variables/features (mutable structured ndarray).
varp	Pairwise annotation of variables/features, a mutable mapping with array-like values.