def _get_shaped_data(
adata: AnnData,
per: str,
annotations: Annotations,
*,
shape: Tuple[int, ...],
name: Union[str, utt.Shaped],
) -> Any:
if isinstance(name, str):
if per == "vo" and name == "__x__":
data = _fix_data(adata.X)
else:
if name not in annotations: # type: ignore
raise _unknown_data(adata, name, per)
data = _fix_data(annotations[name])
if not utt.frozen(data):
utt.freeze(data)
else:
if utt.is_1d(name):
data = utt.to_numpy_vector(name)
else:
data = utt.to_proper_matrix(name) # type: ignore
assert data.shape == shape
return data
def get_vo_frame(
adata: AnnData,
name: Union[str, utt.Matrix] = "__x__",
*,
layout: Optional[str] = None,
formatter: Optional[Callable[[Any], Any]] = None,
) -> utt.PandasFrame:
"""
Get per-variable-per-observation (per-gene-per-cell) data as a pandas data frame.
Rows are observations (cells), indexed by the observation names (typically cell barcode).
Columns are variables (genes), indexed by their names.
If ``name`` is a string, it is the name of a per-variable annotation to fetch.
Otherwise, it should be some matrix of data of the appropriate size.
If ``layout`` (default: {layout}) is specified, it must be one of ``row_major`` or
``column_major``. If this requires relayout of the data, the result is cached in a hidden data
member for future reuse.
"""
data = _get_vo_data(adata, name, layout=layout, formatter=formatter)
frame = utt.maybe_pandas_frame(data)
if frame is None:
frame = utt.to_pandas_frame(utt.to_proper_matrix(data),
index=adata.obs_names,
columns=adata.var_names)
return frame
def get_va_frame(
adata: AnnData,
name: Union[str, utt.Matrix],
*,
columns: Optional[Collection],
layout: Optional[str] = None,
formatter: Optional[Callable[[Any], Any]] = None,
) -> utt.PandasFrame:
"""
Get per-variable-per-any (per-cell-per-any) data as a pandas data frame.
Rows are variables (genes), indexed by their names.
Columns are "something" - specify ``columns`` to specify an index.
If ``name`` is a string, it is the name of a per-variable annotation to fetch.
Otherwise, it should be some matrix of data of the appropriate size.
If ``layout`` (default: {layout}) is specified, it must be one of ``row_major`` or
``column_major``. If this requires relayout of the data, the result is cached in a hidden data
member for future reuse.
"""
data = _get_va_data(adata, name, layout=layout, formatter=formatter)
frame = utt.maybe_pandas_frame(data)
if frame is None:
frame = utt.to_pandas_frame(utt.to_proper_matrix(data),
index=adata.var_names,
columns=columns)
return frame
def get_vo_proper(
adata: AnnData,
name: Union[str, utt.Matrix] = "__x__",
*,
layout: Optional[str] = None,
formatter: Optional[Callable[[Any], Any]] = None,
) -> utt.ProperMatrix:
"""
Same as ``get_vo_data`` but returns a :py:const:`metacells.utilities.typing.ProperMatrix`.
"""
data = _get_vo_data(adata, name, layout=layout, formatter=formatter)
return utt.to_proper_matrix(data, default_layout=layout or "row_major")