grassp.pl.mr_plot

mr_plot(data, mr_key='mr_scores', ax=None, m_cutoffs=[2, 3, 4], r_cutoffs=[0.68, 0.81, 0.93], highlight_hits=True, highlight_proteins=[], show=None, save=None, **kwargs)

MR-plot for simultaneous visualisation of M and R scores.

M corresponds to -log10(q-value) and reflects statistical significance; R is a measure of consistencey of the re-localisation between replicates.

Parameters:

data AnnData

AnnData object after grassp.tl.mr_score().

mr_key str (default: 'mr_scores')

Prefix of the keys written by mr_score (defaults to "mr_scores" resulting in mr_scores_M and mr_scores_R in .obs).

m_cutoffs list[float] (default: [2, 3, 4])

Horizontal/vertical guideline positions (lenient → stringent).

r_cutoffs list[float] (default: [0.68, 0.81, 0.93])

Horizontal/vertical guideline positions (lenient → stringent).

highlight_hits bool (default: True)

If True mark proteins passing the lenient thresholds in red.

highlight_proteins list[str] (default: [])

List of proteins to highlight. Not compatible with highlight_hits.

ax Axes (default: None)

Standard matplotlib/scanpy plotting options.

show bool | None (default: None)

Standard matplotlib/scanpy plotting options.

save bool | str | None (default: None)

Standard matplotlib/scanpy plotting options.

**kwargs

Standard matplotlib/scanpy plotting options.

Return type:

Axes | None

Returns:

Returns the Axes object if show is False.