grassp.pl.bait_volcano_plots

bait_volcano_plots(data, baits=None, sig_cutoff=0.05, lfc_cutoff=2, n_cols=3, base_figsize=5, annotate_top_n=10, color_by=None, highlight=None, title=None, show=False)

Volcano plots for enrichment of pull-down baits.

Parameters:

data AnnData

AnnData object where variables correspond to bait experiments and observations to proteins. A layer named "pvals" must contain the per-protein p-values.

baits Optional[List[str]] (default: None)

Names of the bait columns to visualise. By default all variables are plotted.

sig_cutoff float (default: 0.05)

Thresholds for statistical significance and magnitude (log2 fold change).

lfc_cutoff float (default: 2)

Thresholds for statistical significance and magnitude (log2 fold change).

n_cols int (default: 3)

Layout parameters for the multi-panel figure.

base_figsize float (default: 5)

Layout parameters for the multi-panel figure.

annotate_top_n int (default: 10)

Annotate the n proteins with the smallest p-values.

color_by str | None (default: None)

Optional observation annotation used for point color.

highlight Optional[List[str]] (default: None)

Protein IDs to emphasise across all panels.

title str | None (default: None)

Suptitle for the figure.

show bool (default: False)

If True (default) the figure is displayed; otherwise the array of Axes is returned.

Return type:

Axes | None

Returns:

Returns the array of Axes (when show is False) or None.