muon.MuData

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

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

Parameters:

• data – AnnData object or dictionary with AnnData objects as values. If a dictionary is passed, the keys will be used as modality names.

• 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.

Methods

__init__([data, feature_types_names, ...])	param data: AnnData object or dictionary with AnnData objects as values.
copy([filename])	Make a copy.
obs_keys()	List keys of observation annotation obs.
obs_names_make_unique()	Call .obs_names_make_unique() method on each AnnData object.
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 the data from the modalities to the global .obs, existing columns to be overwritten or updated
pull_var([columns, mods, common, ...])	Copy the data from the modalities to the global .var, existing columns to be overwritten or updated
push_obs([columns, mods, common, prefixed, ...])	Copy the data from the mdata.obs to the modalities, existing columns to be overwritten
push_var([columns, mods, common, prefixed, ...])	Copy the data from the mdata.var to the modalities, existing columns to be overwritten
strings_to_categoricals([df])	Transform string columns in .var and .obs slots of MuData to categorical as well as of .var and .obs slots in each AnnData object
to_anndata(**kwargs)	Convert MuData to AnnData
uns_keys()	List keys of unstructured annotation.
update()	Update both .obs and .var indices of MuData with the data from all the modalities
update_obs()	Update global .obs_names according to the .obs_names of all the modalities.
update_var()	Update global .var_names according to the .var_names of all the modalities.
var_keys()	List keys of variable annotation var.
var_names_make_unique()	Call .var_names_make_unique() method on each AnnData object.
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 MuData object to an HDF5 file
write_h5mu([filename])	Write MuData object to an HDF5 file
write_zarr(store, **kwargs)	Write MuData object to a Zarr store

Attributes

axis	MuData axis
filename	Filename of the MuData object.
isbacked	Whether the MuData object is backed.
mod_names	Names of modalities (alias for list(mdata.mod.keys()))
n_mod	Number of modalities in the MuData object.
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 observation
obsmap	Mapping of observation index in the MuData to indices in individual modalities.
obsp	Pairwise annotatation of observations
shape	Shape of data, all variables and observations combined (n_obs, n_var).
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 index in the MuData to indices in individual modalities.
varp	Pairwise annotatation of variables