omicverse.metabol.pathway_bar

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omicverse.metabol.pathway_bar#

omicverse.metabol.pathway_bar(enrichment, *, term_col=None, score_col='pvalue', top_n=15, ax=None, figsize=(6.0, 5.0))[source]#

Horizontal bar chart of pathway enrichment p-values.

Works for both msea_ora output (pathway / pvalue) and lion_enrichment output (term / pvalue); auto-detects the term column if term_col isn’t given.

Parameters:

  • enrichment (DataFrame) – DataFrame returned by msea_ora(), msea_gsea(), or lion_enrichment().

  • term_col (Optional[str] (default: None)) – Column holding the pathway / term name. Auto-picks from pathway / term / Term / the index if None.

  • score_col (str (default: 'pvalue')) – Column to plot. "pvalue" (default) → -log10(pvalue) bars; "padj" for FDR-adjusted; "nes" for GSEA normalized enrichment score (plotted as-is, signed).

  • top_n (int (default: 15)) – Show the top-top_n terms by the score.

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