anndict.adata_dict.adata_dict.AdataDict

class anndict.adata_dict.adata_dict.AdataDict(data=None, hierarchy=None)

AdataDict is a dictionary-like container where values are AnnData objects. AdataDict inherits from dict.

This class provides three main functionalities:

1. It has the set_hierarchy method to restructure the nesting hierarchy, and the hierarchy attribute to keep track.

2. It behaves like an AnnData object by passing methods through to each AnnData in the dictionary.

3. It has methods fapply(func, kwargs) and fapply_return(func, kwargs) that apply a given function func with arguments kwargs to each AnnData object in the AdataDict.

Parameters:

data dict[tuple[int, ...], any] | None (default: None)

Dictionary with keys as tuples of indices.

hierarchy tuple | list | None (default: None)

Tuple or list indicating the order of indices in the keys of data.

__init__(data=None, hierarchy=None)

Initialize the AdataDict with data and hierarchy.

Parameters:

data dict[tuple[int, ...], any] | None (default: None)

Dictionary with keys as tuples of indices.

hierarchy tuple | list | None (default: None)

Tuple or list indicating the order of indices.

Returns:

None Initializes the AdataDict object.

Return type:

None

Methods

__init__([data, hierarchy])	Initialize the AdataDict with data and hierarchy.
clear()
copy()	Copy the AdataDict.
fapply(func, *[, use_multithreading, ...])	Applies func to each AnnData in adata_dict, with error handling, retry mechanism, and the option to use either threading or sequential execution.
fapply_return(func, *[, use_multithreading, ...])	Legacy wrapper for adata_dict_fapply.
flatten()	Flatten the hierarchy of AdataDict.
flatten_nesting_list(nesting_list)	Flatten a nested list or tuple into a single list.
fromkeys([value])	Create a new dictionary with keys from iterable and values set to value.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
get_levels(nesting_list[, levels, depth])	Get the levels of hierarchy based on the nesting structure.
items()
keys()
pop(k[,d])	If the key is not found, return the default if given; otherwise, raise a KeyError.
popitem()	Remove and return a (key, value) pair as a 2-tuple.
set_hierarchy(nesting_list)	Rearrange the hierarchy of AdataDict based on the provided nesting structure.
set_obs_index(column)	Set the index of adata.obs to the specified column for each AnnData object in adata_dict.
set_var_index(column)	Set the index of adata.var to the specified column for each AnnData in adata_dict.
setdefault(key[, default])	Insert key with a value of default if key is not in the dictionary.
update([E, ]**F)	If E is present and has a .keys() method, then does: for k in E.keys(): D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
values()

Attributes

hierarchy

The hierarchy of the AdataDict.