opendvp.pl.volcano

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opendvp.pl.volcano#

volcano(adata, x='mean_diff', y='-log10_p_corr', significant=False, FDR=None, significant_metric='p_corr', tag_top=None, group1=None, group2=None, return_fig=False, ax=None, highlight_genes=None, show_highlighted_genes_names=True, **kwargs)#

Plot a volcano plot from an AnnData object.

Parameters:

  • adata (anndata.AnnData) – An AnnData object with statistical test results stored in adata.var.

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

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

  • significant (bool) – Whether to highlight significant points based on FDR threshold.

  • FDR (float or None) – Threshold for corrected p-value (e.g., 0.05). Required if significant=True.

  • tag_top (int or None) – Number of top hits (by y) to label with text, regardless of significance.

  • group1 (str or None) – Name of the first group (used for x-axis label annotation).

  • group2 (str or None) – Name of the second group (used for x-axis label annotation).

  • return_fig (bool) – If True, returns the matplotlib fig object for further modification.

  • highlight_genes (list or None) – List of gene names/IDs to highlight and label on the plot, if present in adata.var.index.

  • show_highlighted_genes_names (bool) – If True, shows names of highlighted genes on the plot.

  • ax (matplotlib.axes.Axes, optional) – Axes object to plot on. If None, a new figure and axes are created.

  • **kwargs (Mapping[str, Any]) – Additional keyword arguments passed to matplotlib scatter.

Returns:

fig – The fig object if return_fig=True, otherwise None.

Return type:

matplotlib.figure.Figure or None

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