scirpy.tl.spectratype

scirpy.tl.spectratype(adata, chain='VJ_1', *, target_col, cdr3_col='junction_aa', combine_fun=<function sum>, fraction=None, airr_mod='airr', airr_key='airr', chain_idx_key='chain_indices', **kwargs)

Summarizes the distribution of CDR3 region lengths.

Ignores NaN values.

Parameters

adata : AnnData | MuData | DataHandlerUnion[AnnData, MuData, DataHandler]

AnnData or MuData object that contains AIRR information.

chain : {‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’} | Sequence[Literal[‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’]]Union[Literal[‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’], Sequence[Literal[‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’]]] (default: 'VJ_1')

One or multiple chains from which to use CDR3 sequences

target_col : str

Color by this column from obs. E.g. sample or diagnosis

cdr3_col : str (default: 'junction_aa')

AIRR rearrangement column from which sequences are obtained

combine_fun : Callable (default: <function sum at 0x000001123C0631F0>)

A function definining how the groupby columns should be merged (e.g. sum, mean, median, etc).

fraction : str | bool | NoneUnion[str, bool, None] (default: None)

If True, compute fractions of abundances relative to the groupby column rather than reporting abosolute numbers. Alternatively, a column name can be provided according to that the values will be normalized.

airr_mod

Name of the modality with AIRR information is stored in the MuData object. if an AnnData object is passed to the function, this parameter is ignored.

airr_key

Key under which the AIRR information is stored in adata.obsm as an awkward array.

chain_idx_key

Key under which the chain indices are stored in adata.obsm. If chain indices are not present, index_chains() is run with default parameters.

Return type

DataFrame

Returns

A DataFrame with spectratype information.