feat(dataProcessPlots): Add confidence interval bars to profile plots

[tonywu1999]

Motivation and Context

We should add confidence intervals for MSstats+

Changes

• If the variance column exists in the quantitative output of dataProcess, then add confidence interval bars to profile plot

Testing

• Verified confidence intervals were added when variance column exists, and none otherwise.
• Tested with MSstats+ vignette.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• I have run the devtools::document() command after my changes and committed the added files

Summary by CodeRabbit

• New Features

  • Profile plots now show 95% confidence-like intervals as error bars on peptide run summary plots when variance is available, highlighting uncertainty around intensity measurements.

• Documentation

  • Vignette updated with a paragraph and example demonstrating the new profile-plot visualization and how to call it for summarized data.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

Adds LOWERBOUND and UPPERBOUND to Run summary data when Variance exists, and renders them as error bars in the Run summary branch of the profile plot for censored analyses; vignette updated with an example for the ProfilePlot.

Changes

Cohort / File(s)	Summary
Summary Data Preparation R/dataProcessPlots.R	Adds UPPERBOUND and LOWERBOUND fields computing ~95% confidence-like intervals around LogIntensities when Variance is present; otherwise NA_real_.
Visualization Layer R/utils_dataprocess_plots.R	In .makeSummaryProfilePlot, when is_censored is TRUE adds a geom_errorbar for the "Run summary" peptide subset mapping ymin=LOWERBOUND, ymax=UPPERBOUND, and color=analysis.
Documentation / Example vignettes/MSstatsPlus.Rmd	Adds descriptive text and a code example showing ProfilePlot visualization of variance via the new confidence-interval-like bounds.

Sequence Diagram(s)

(omitted — changes are localized to data preparation and plotting code; no multi-component sequential flow requiring visualization)

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• fix(dataProcessPlots, groupComparisonPlots): Migrate away from deprecated functions for ggplot #175: Modifies ggplot aesthetics in R/utils_dataprocess_plots.R, overlapping with the plotting code changed here.

Suggested labels

Review effort 2/5

Suggested reviewers

• devonjkohler
• mstaniak
• anshuman-raina

Poem

🐰 I nibbled through data, hop by hop,
Boundaries drawn where variances stop.
Little bars show where numbers hide,
Run summaries beam with interval pride. 🎨📈

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: adding confidence interval bars to profile plots in dataProcessPlots function.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The PR description follows the required template with all key sections present: motivation, detailed changes list, testing description, and completed checklist.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

• 📝 Generate docstrings

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[github-actions]

Failed to generate code suggestions for PR