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featureMSEA Tutorial: Feature-based Metabolite Set Enrichment Analysis

11 Visualization

11.1 Step 6 — Plot enrichment results

plot_fmsea_plot() generates a multi-panel enrichment plot for a single pathway of interest.

# Plot enrichment results for a specific pathway
plot_fmsea_plot(
  fmsea_obj  = fmsea_result,
  pathway_id = "hsa00010",                  # pathway ID from significant_modules
  title      = "Glycolysis / Gluconeogenesis"
)

The plot includes four panels:

  1. Enrichment score curve — the running enrichment score across the ranked feature list, with the peak marking the leading-edge boundary.
  2. Ranked feature hits — vertical bars showing where features annotated to pathway metabolites fall in the ranked list.
  3. Annotation weights — per-feature annotation confidence scores.
  4. Pair weights — feature–metabolite pair weights used in the enrichment scoring.

To find valid pathway_id values, inspect the significant modules table:

# View significant pathways and their IDs
head(fmsea_result@significant_modules)

11.2 Saving results

Export the full result object for later use or to resume analysis in the Shiny app:

# Save result object
save(fmsea_result, file = "fmsea_result.rda")

The saved fmsea_result.rda file can be uploaded directly to the Shiny app’s Data Upload panel to skip re-running annotation and enrichment and proceed straight to interactive visualization.