liana.ms.mdata_to_anndata

liana.ms.mdata_to_anndata(mdata, x_mod, y_mod, x_layer=None, y_layer=None, x_use_raw=False, y_use_raw=False, x_transform=None, y_transform=None, verbose=True)

Convert a MultiData object to an AnnData object.

Parameters:

mdata MuData

MuData object.

x_mod str

Name of the modality to be used as x.

y_mod str

Name of the modality to be used as y.

x_layer str | None (default: None)

Layer to be used for modality x.

y_layer str | None (default: None)

Layer to be used for modality y.

x_use_raw bool (default: False)

Whether to use raw counts for modality x.

y_use_raw bool (default: False)

Whether to use raw counts for modality y.

x_transform Callable[[NDArray[number] | csc_matrix | csr_matrix | csc_array | csr_array], NDArray[number] | csc_matrix | csr_matrix | csc_array | csr_array] | None (default: None)

Transformation function to be applied to modality x.

y_transform Callable[[NDArray[number] | csc_matrix | csr_matrix | csc_array | csr_array], NDArray[number] | csc_matrix | csr_matrix | csc_array | csr_array] | None (default: None)

Transformation function to be applied to modality y.

verbose bool (default: True)

Verbosity flag.

Return type:

AnnData

Returns:

An AnnData object with the two modalities concatenated. Information related to observations (obs, obsp, obsm) and .uns are copied from the original MuData object.

Raises:

ValueError – If x_mod and/or y_mod are not provided.

Examples

Joins two modalities of a MuData along the variable axis, which is what liana.mt.bivariate expects when relating one modality to another:

>>> import liana as li
>>> mdata = li.ds.generate_toy_mdata()
>>> adata = li.ms.mdata_to_anndata(mdata, x_mod="adata_x", y_mod="adata_y", x_layer="scaled", y_layer="scaled")