scirpy.pl.spectratype
- scirpy.pl.spectratype(adata, cdr3_col=['IR_VJ_1_junction_aa'], *, color, combine_fun=<function sum>, normalize=None, viztype='bar', kde_kws=None, **kwargs)
Show the distribution of CDR3 region lengths.
`
Show the distribution of CDR3 region lengths.
Ignores NaN values.
- Parameters
- adata :
dict|AnnDataUnion[dict,AnnData] AnnData object to work on.
- cdr3_col :
str|Collection[str]Union[str,Collection[str]] (default:['IR_VJ_1_junction_aa']) Column(s) containing CDR3 lengths.
- color :
str Color by this column from
obs. E.g. sample or diagnosis- combine_fun :
Callable(default:<function sum at 0x00000277B4191670>) A function definining how the
cdr3_colcolumns should be merged, in case multiple ones were specified. (e.g. sum, mean, median, etc).- normalize :
None|str|boolUnion[None,str,bool] (default:None) If True, compute fractions of abundances relative to the
cdr3_colcolumn rather than reporting abosolute numbers. Alternatively, the name of a column containing a categorical variable can be provided according to which the values will be normalized.- viztype : {‘bar’, ‘line’, ‘curve’}
Literal[‘bar’, ‘line’, ‘curve’] (default:'bar') Type of plot to produce.
- **kwargs
Additional parameters passed to the base plotting function
- adata :
- Return type
- Returns
Axes object