omicverse.metabol.volcano

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omicverse.metabol.volcano#

omicverse.metabol.volcano(deg, *, padj_thresh=0.05, log2fc_thresh=1.0, label_top_n=10, use_pvalue=False, clip_log2fc=None, ax=None, figsize=(5.5, 4.5))[source]#

Metabolomics volcano plot — log2FC vs -log10(padj) (or pvalue).

Parameters:

  • use_pvalue (bool (default: False)) – Plot against the raw pvalue column instead of the BH-adjusted padj. Useful for small-n untargeted LC-MS where the 5000+ feature FDR burden means no peak survives FDR; raw p-value is the honest axis for the volcano in that regime.

  • clip_log2fc (Optional[float] (default: None)) – Clip the x-axis to ±this value. On LC-MS data with below-detection zeros, a handful of features can have log2fc up to ±25 after pseudo-count logging and completely dominate the plot. Set e.g. clip_log2fc=5 to keep the volcano interpretable.

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