vampire.anno.pl.logo

vampire.anno.pl.logo(adata, feature='information', *, drop_gap=False, colormap=None, conserved_color='#cccccc', title='', figsize=(None, None), save=None, **kwargs)

Plot the logo plot from anndata object.

Parameters:

• adata (AnnData) – The AnnData object.

• feature (Literal['count', 'probability', 'information']) – The feature to show. Default is “information”.

• drop_gap (bool) – If True, exclude gap (“-”) from counting and plotting. Only A/C/G/T are shown. Default is False (backward-compatible).

• colormap (dict | None) – The colors of the bases. Default is None, using the default colormap.

• conserved_color (str | None) – Override color for conserved sites (non-variant positions). Default is “#cccccc”. If set to None, conserved sites will use the general base color instead.

• title (str) – The title of the plot. Default is empty.

• figsize (tuple[int | None, int | None] | None) – Figure size as (width, height) in pixels. Default is (None, None).

• save (str | bool | None) – If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.

• **kwargs – Additional keyword arguments passed to Plotly update_layout. Used to control figure-level styling (e.g. template, margin, background color, legend settings).

Returns:

The logo figure.

Return type:

Figure

Examples

>>> import vampire as vp
>>> vp.anno.pl.set_default_plotstyle()
>>> adata = vp.datasets.wdr7_hprc()
>>> vp.anno.tl.motif_msa(adata)
>>> vp.anno.pl.logo(
...     adata,
...     feature = "information"
... )