scirpy.tl.clonotype_imbalance
- scirpy.tl.clonotype_imbalance(adata, replicate_col, groupby, case_label, *, control_label=None, target_col='clone_id', additional_hue=None, fraction=None, inplace=True, overlap_key=None, key_added='clonotype_imbalance', airr_mod='airr')
Aims to find clonotypes that are the most enriched or depleted in a category.
Uses Fischer’s exact test to rank clonotypes. Depends on execution of
scirpy.tl.repertoire_overlap()
. Adds two dataframes (abundance of clonotypes per sample; pval and logFC for clonotypes) touns
Warning
This is an experimental function and will likely change in the future.
- Parameters
- adata :
AnnData
|MuData
|DataHandler
Union
[AnnData
,MuData
,DataHandler
] AnnData or MuData object that contains AIRR information.
- replicate_col :
str
Column with batch or sample labels.
- groupby :
str
The column containing categories that we want to compare and find imbalance between
- case_label :
str
The label in
groupby
column that we want to compare.- control_label :
str
|None
Optional
[str
] (default:None
) The label in
groupby
column that we use as a baseline for comparison. If not set (None by default), all labels that are not equal tocase_label
make up the baseline.- target_col :
str
(default:'clone_id'
) The clusters (clonotypes by default) that are imbalanced.
- additional_hue :
str
|bool
|None
Union
[str
,bool
,None
] (default:None
) An additional grouping factor. If the
case_label
was tumor for example, this could help make a distinction between imbalance in lung and colorectal tumors.- fraction :
str
|bool
|None
Union
[str
,bool
,None
] (default:None
) If
True
, compute fractions of abundances relative to thegroupby
column rather than reporting abosolute numbers. Alternatively, a column name can be provided according to that the values will be normalized or an iterable providing cell weights directly. Setting it toFalse
orNone
assigns equal weight to all cells.- inplace :
bool
(default:True
) Whether results should be added to
uns
or returned directly.- overlap_key :
str
|None
Optional
[str
] (default:None
) Under what key should the repertoire overlap results be looked up in
uns
. By default it is None to ensure that the overlap tool is executed with the right parameters.- key_added :
str
(default:'clonotype_imbalance'
) Results will be added to
uns
under this key.- airr_mod :
str
(default:'airr'
) Name of the modality with AIRR information is stored in the
MuData
object. if anAnnData
object is passed to the function, this parameter is ignored.
- adata :
- Return type
None
|Tuple
[DataFrame
,DataFrame
]Optional
[Tuple
[DataFrame
,DataFrame
]]- Returns
Two dataframes: abundance of clonotypes per sample; pval and logFC for clonotypes.