scirpy.pl.vdj_usage

scirpy.pl.vdj_usage(adata, *, vdj_cols=['TRA_1_j_gene', 'TRA_1_v_gene', 'TRB_1_v_gene', 'TRB_1_d_gene', 'TRB_1_j_gene'], normalize_to=None, ax=None, bar_clip=5, top_n=10, barwidth=0.4, draw_bars=True, full_combination=True, fig_kws=None)

Creates a ribbon plot of the most abundant VDJ combinations.
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Creates a ribbon plot of the most abundant VDJ combinations.

Currently works with primary alpha and beta chains only.

Parameters

adata : AnnDataAnnData

AnnData object to work on.

vdj_cols : listlist (default: ['TRA_1_j_gene', 'TRA_1_v_gene', 'TRB_1_v_gene', 'TRB_1_d_gene', 'TRB_1_j_gene'])

Columns containing gene segment information. Overwrite default only if you know what you are doing!

normalize_to : None, str, Sequence[float]Union[None, str, Sequence[float]] (default: None)

Either the name of a categorical column that should be used as the base for computing fractions, or an iterable specifying a size factor for each cell. By default, each cell count as 1, but due to normalization to different, for instance, sample sizes, it is possible that one cell in a small sample is weighted more than a cell in a large sample.

ax : Axes, NoneOptional[Axes] (default: None)

Custom axis if needed.

bar_clip : intint (default: 5)

The maximum number of stocks for bars (number of different V, D or J segments that should be shown separately).

top_n : None, intOptional[int] (default: 10)

The maximum number of ribbons (individual VDJ combinations). If set to None, all ribbons are drawn.

barwidth : floatfloat (default: 0.4)

Width of bars.

draw_bars : boolbool (default: True)

If False, only ribbons are drawn and no bars.

full_combination : boolbool (default: True)

If set to False, the bands represent the frequency of a binary gene segment combination of the two connectec loci (e.g. combination of TRBD and TRBJ genes). By default each band represents an individual combination of all five loci.

fig_kws : dict, NoneOptional[dict] (default: None)

Dictionary of keyword args that will be passed to the matplotlib figure (e.g. figsize)

Return type

AxesAxes

Returns

Axes object.