omicverse.metabol.pathway_dot

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omicverse.metabol.pathway_dot#

omicverse.metabol.pathway_dot(enrichment, *, term_col=None, size_col='overlap', x_col='odds_ratio', color_col='pvalue', top_n=15, ax=None, figsize=(6.5, 5.5))[source]#

Dot plot of pathway enrichment — the de-facto standard figure.

Matches the layout of scanpy’s / clusterProfiler’s dot plot: each row is a pathway, dot size encodes overlap count, x position encodes fold-enrichment (odds ratio or NES), color encodes -log10(p-value).

Parameters:

  • size_col (str (default: 'overlap')) – Column mapped to dot size. Default "overlap" (ORA output); use "matched_size" for GSEA output.

  • x_col (str (default: 'odds_ratio')) – Column mapped to x position. Default "odds_ratio" (ORA); use "nes" for GSEA.

  • color_col (str (default: 'pvalue')) – Column mapped to color (via -log10). Default "pvalue".

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