muon.MuData

class muon.MuData(data: AnnData | Mapping[str, AnnData] | MuData | None = None, feature_types_names: Mapping[str, str] | None = mappingproxy({'Gene Expression': 'rna', 'Peaks': 'atac', 'Antibody Capture': 'prot'}), as_view: bool = False, index: tuple[slice | int, slice | int] | slice | int | None = None, **kwargs)

Multimodal data object

MuData represents modalities as collections of AnnData objects as well as includes multimodal annotations such as embeddings and neighbours graphs learned jointly on multiple modalities and generalised sample and feature metadata tables.

Parameters:

• data – AnnData object or dictionary with AnnData objects as values. If a dictionary is passed, the keys will be used as modality names. If None, creates an empty MuData object.

• feature_types_names – Dictionary to map feature types encoded in data.var[“feature_types”] to modality names. Only relevant when data is an AnnData object. Default: {“Gene Expression”: “rna”, “Peaks”: “atac”, “Antibody Capture”: “prot”}

• as_view – Create a view of the MuData object.

• index – Index to slice the MuData object when creating the view.

• **kwargs – Additional arguments to create a MuData object.

__init__(data: AnnData | Mapping[str, AnnData] | MuData | None = None, feature_types_names: Mapping[str, str] | None = mappingproxy({'Gene Expression': 'rna', 'Peaks': 'atac', 'Antibody Capture': 'prot'}), as_view: bool = False, index: tuple[slice | int, slice | int] | slice | int | None = None, **kwargs)

Methods

__init__([data, feature_types_names, ...])
copy([filename])	Make a copy.
obs_keys()	List keys of observation annotation obs.
obs_names_make_unique()	Call AnnData.obs_names_make_unique on each modality.
obs_vector(key[, layer])	Return an array of values for the requested key of length n_obs.
obsm_keys()	List keys of observation annotation obsm.
pull_obs([columns, mods, common, ...])	Copy data from the obs of the modalities to the global obs
pull_var([columns, mods, common, ...])	Copy data from the var of the modalities to the global var
push_obs([columns, mods, common, prefixed, ...])	Copy the data from obs to the obs of the modalities.
push_var([columns, mods, common, prefixed, ...])	Copy the data from var to the var of the modalities.
strings_to_categoricals([df])	Transform string annotations to categoricals.
to_anndata(**kwargs)	Convert the object to AnnData.
uns_keys()	List keys of unstructured annotation.
update()	Update both obs and var indices of the object with the data from all the modalities.
update_obs()	Update obs indices of the object with the data from all the modalities.
update_var()	Update var indices of the object with the data from all the modalities.
var_keys()	List keys of variable annotation var.
var_names_make_unique()	Call AnnData.var_names_make_unique on each modality.
var_vector(key[, layer])	Return an array of values for the requested key of length n_var.
varm_keys()	List keys of variable annotation varm.
write([filename])	Write the object to an HDF5 file.
write_h5mu([filename])	Write the object to an HDF5 file.
write_zarr(store, **kwargs)	Write the object to a Zarr store.

Attributes

axis	MuData axis.
filename	Change the backing mode by setting the filename to a .h5mu file.
is_view	Whether the object is a view of another MuData object.
isbacked	Whether the object is backed on disk.
mod	Dictionary of modalities.
mod_names	Names of modalities (alias for list(mdata.mod.keys()))
n_mod	Number of modalities.
n_obs	Total number of observations
n_var	Total number of variables.
n_vars	Total number of variables.
obs	Annotation of observation
obs_names	Names of variables (alias for .obs.index).
obsm	Multi-dimensional annotation of observations.
obsmap	Mapping of observation indices in the object to indices in individual modalities.
obsp	Pairwise annotatation of observations.
shape	Shape of data, all variables and observations combined (n_obs, n_vars).
uns	Unstructured annotation (ordered dictionary).
var	Annotation of variables.
var_names	Names of variables (alias for .var.index)
varm	Multi-dimensional annotation of variables.
varmap	Mapping of feature indices in the object to indices in individual modalities.
varp	Pairwise annotatation of variables.