mantispy.pl.pathway_coherence

mantispy.pl.pathway_coherence(adata, key='pathway_coherence', top=15, ax=None)

Coherence per gene set, the significant ones marked.

Sets are ordered by coherence, as in the table. Under a permutation null every coherent set ties at the p-value floor, so the q-value marks significance and coherence ranks the sets.

Parameters:

• adata (AnnData) – Object holding the table pathway_coherence() wrote.

• key (str (default: 'pathway_coherence')) – Name of that table in uns["mantispy"].

• top (int (default: 15)) – How many sets to draw, taken by coherence.

• ax (Axes | None (default: None)) – Axes to draw on, or None for a new figure.

Return type:

Axes | None

Returns:

The axes when the caller passed ax, else None because the plot then owns the figure it created. When returned they hold one bar per set labeled by how many of its genes were in the screen, colored by whether its q-value is below 0.05.

Raises:

• KeyError – uns["mantispy"] holds no table under key.

• ValueError – That table is empty, which is what happens when no set had enough of its genes in the screen.