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)

Methods

__init__([data, feature_types_names, ...])
copy([filename])
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.
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
uns_keys()	List keys of unstructured annotation.
update()	Update both .obs and .var of MuData with the data from all the modalities
update_obs()	Update .obs slot of MuData with the newest .obs data from all the modalities
update_var()	Update .var slot of MuData with the newest .var data from 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
isbacked
n_mod
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).
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