snapatac2.AnnData

class snapatac2.AnnData(*, filename, X=None, obs=None, var=None, obsm=None, varm=None, uns=None, backend=None)

An annotated data matrix.

AnnData stores a data matrix X together with annotations of observations obs (obsm, obsp), variables var (varm, varp), and unstructured annotations uns. AnnData is stored as a HDF5 file. Opening/creating an AnnData object does not read data from the HDF5 file. Data is copied to memory only when individual element is requested (or when cache is turned on).

Parameters:

• X – A #observations × #variables data matrix. A view of the data is used if the data type matches, otherwise, a copy is made.

• obs – Key-indexed one-dimensional observations annotation of length #observations.

• var – Key-indexed one-dimensional variables annotation of length #variables.

• uns – Key-indexed unstructured annotation.

• obsm – Key-indexed multi-dimensional observations annotation of length #observations. If passing a ndarray, it needs to have a structured datatype.

• varm – Key-indexed multi-dimensional variables annotation of length #variables. If passing a ndarray, it needs to have a structured datatype.

• filename – Name of backing file.

Note

This is a backed AnnData. You can use to_memory to convert it to an in-memory AnnData object. See here for the documentation of in-memory AnnData objects.

See also

read, read_mtx, read_csv

Attributes

X	Data matrix of shape n_obs × n_vars.
backend
filename	Filename of the backing .h5ad file.
isbacked	Whether the AnnData object is backed.
layers
n_obs	Number of observations.
n_vars	Number of variables/features.
obs	Observation annotations.
obs_names	Names of observations.
obsm
obsp
shape	Shape of data matrix (n_obs, n_vars).
uns	Unstructured annotation (ordered dictionary).
var	Variable annotations.
var_names	Names of variables.
varm
varp

Methods

chunked_X([chunk_size])	Return an iterator over the rows of the data matrix X.
close()	Close the AnnData object.
copy(filename, backend)	Copy the AnnData object.
is_closed()	If the AnnData object has been closed.
obs_ix(names)
open([mode])	Reopen a closed AnnData object.
subset([obs_indices, var_indices, out, backend])	Subsetting the AnnData object.
to_memory()	Return a new AnnData object with all backed arrays loaded into memory.
var_ix(names)
write(filename, backend)	Write .h5ad-formatted hdf5 file.