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