Template-gate the results-table column headers for metabolomics

[swaraj-neu]

Motivation and Context

Metabolomics templates require user-facing results-table headers to use “Metabolite” instead of “Protein”. The original data must remain unchanged for downstream processing and CSV downloads.

The change adds template-aware display renaming and passes the active application template to relevant table-rendering paths.

Changes

• Added rename_protein_column_for_display() to rename Protein to Metabolite for metabolomics templates.
• Preserved the input data during display renaming.
• Updated significant-proteins table rendering to use template-aware column names.
• Passed the reactive app_template to render_results_table().
• Applied display renaming to the QC abundance data table.
• Kept CSV downloads unchanged.
• Added a default app_template to render_results_table().
• Imported updateRadioButtons from shiny.
• Updated visualizeNetworkServer documentation and signature to accept an optional reactive app_template.

Tests

• No unit tests were added or modified.

Coding Guidelines

• No coding guideline violations were identified.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 9a042f42-ee1d-473f-ab48-066befa5d884

📥 Commits

Reviewing files that changed from the base of the PR and between 359152d and 4069da4.

📒 Files selected for processing (1)

• R/utils.R

🚧 Files skipped from review as they are similar to previous changes (1)

• R/utils.R

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📝 Walkthrough

Walkthrough

The change adds template-aware protein-column display handling for significant-protein and abundance tables, propagates app_template through result rendering, documents the updated server interface, and imports updateRadioButtons into the package namespace.

Changes

Template-aware display

Layer / File(s)	Summary
Template-aware display helper and table rendering R/utils.R, R/statmodel-server-results-table.R, R/qc-server-summary.R	Rendered tables copy their data and rename Protein to Metabolite for the metabolomics template. CSV downloads retain the original data.
Template propagation and interface wiring R/module-statmodel-server.R, man/visualizeNetworkServer.Rd, NAMESPACE	Statmodel rendering receives app_template. The documented server interface exposes the optional argument with a default. updateRadioButtons is imported.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• Vitek-Lab/MSstatsShiny#155: Introduced render_results_table, which this change extends.
• Vitek-Lab/MSstatsShiny#219: Added the metabolomics template used by the column-renaming logic.
• Vitek-Lab/MSstatsShiny#223: Also updated visualizeNetworkServer with an app_template argument.

Suggested reviewers: tonywu1999

Poem

A rabbit watches columns align,
Protein becomes Metabolite by design.
Templates guide each rendered view,
CSV data stays unchanged and true.
Shiny imports join the queue.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: template-specific column headers for metabolomics results tables.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch MSstatsShiny/work/20260730_metabolomics_terminology_qc_statmodel

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@R/utils.R`:
- Around line 1147-1150: Update the conditional in
rename_protein_column_for_display to wrap the app_template() comparison with
isTRUE(), so NULL or NA values safely preserve the Protein header while the
metabolomics case still renames it to Metabolite.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 09a5ea31-0b1c-4bf9-9a48-f2a5529cf059

📥 Commits

Reviewing files that changed from the base of the PR and between f494440 and 359152d.

📒 Files selected for processing (6)

• NAMESPACE
• R/module-statmodel-server.R
• R/qc-server-summary.R
• R/statmodel-server-results-table.R
• R/utils.R
• man/visualizeNetworkServer.Rd