def get_v_names(adata: AnnData, ) -> utt.NumpyVector:
"""
Get a numpy vector of variable names.
"""
data = utt.to_numpy_vector(adata.var_names)
utl.log_get(adata, "v", "__name__", data)
return data
def _get_v_data(
adata: AnnData,
name: Union[str, utt.Shaped],
*,
sum: bool, # pylint: disable=redefined-builtin
formatter: Optional[Callable[[Any], Any]] = None,
) -> Any:
if not isinstance(name, str):
log_name = "<data>"
else:
if isinstance(name, str) and name.endswith("|sum"):
name = name[:-4]
assert not sum
sum = True
log_name = name
if sum:
if formatter is None:
formatter = utl.sizes_description
data = _get_vo_sum_data(adata, "column", name)
log_name += "|sum"
else:
data = _get_shaped_data(adata,
"v",
adata.var,
shape=(adata.n_vars, ),
name=name)
utl.log_get(adata, "v", log_name, data, formatter=formatter)
return data
def get_o_names(adata: AnnData, ) -> utt.NumpyVector:
"""
Get a numpy vector of observation names.
"""
data = utt.to_numpy_vector(adata.obs_names)
utl.log_get(adata, "o", "__name__", data)
return data
def get_m_data(
adata: AnnData,
name: str,
*,
formatter: Optional[Callable[[Any], Any]] = None,
) -> Any:
"""
Get metadata (unstructured annotation) in ``adata`` by its ``name``.
"""
data = adata.uns.get(name)
if data is None:
raise _unknown_data(adata, name, "m")
utl.log_get(adata, "m", name, data, formatter=formatter)
return data
def _get_va_data(
adata: AnnData,
name: Union[str, utt.Matrix],
*,
layout: Optional[str] = None,
formatter: Optional[Callable[[Any], Any]] = None,
) -> utt.Matrix:
data = _get_layout_data(adata,
"va",
adata.varm,
shape=(adata.n_vars, 0),
name=name,
layout=layout)
utl.log_get(adata, "va", name, data, formatter=formatter)
return data
def _get_vo_data(
adata: AnnData,
name: Union[str, utt.Matrix],
*,
layout: Optional[str] = None,
formatter: Optional[Callable[[Any], Any]] = None,
) -> utt.Matrix:
if name is None:
name = "__x__"
data = _get_layout_data(adata,
"vo",
adata.layers,
shape=(adata.n_obs, adata.n_vars),
name=name,
layout=layout)
utl.log_get(adata, "vo", name, data, formatter=formatter)
return data