opendvp.plotting.volcano

opendvp.plotting.volcano(adata, x='log2_FC', y='-log10(p_val_corr)_BH', significant=True, FDR=None, tag_top=None, group1=None, group2=None, return_fig=False, highlight_genes=None, show_highlighted_genes_names=True, ax=None, **kwargs)

Plot a volcano plot from an AnnData object.

Return type:

Figure | None

Parameters

adataAnnData

An AnnData object with statistical test results stored in adata.var.

xstr

Column name in adata.var for the x-axis (e.g., log2 fold change).

ystr

Column name in adata.var for the y-axis (e.g., -log10 p-value).

significantbool

Whether to highlight significant points based on FDR threshold.

FDRfloat or None

Threshold for corrected p-value (e.g., 0.05). Required if significant=True.

tag_topint or None

Number of top hits (by y) to label with text, regardless of significance.

group1str or None

Name of the first group (used for x-axis label annotation).

group2str or None

Name of the second group (used for x-axis label annotation).

return_figbool

If True, returns the matplotlib fig object for further modification.

highlight_geneslist or None

List of gene names/IDs to highlight and label on the plot, if present in adata.var.index.

show_highlighted_genes_namesbool

If True, shows names of highlighted genes on the plot.

axmatplotlib.axes.Axes, optional

Axes object to plot on. If None, a new figure and axes are created.

**kwargs

Additional keyword arguments passed to matplotlib scatter.

Returns:

figmatplotlib.figure.Figure or None

The fig object if return_fig=True, otherwise None.