chore(profile-plot): Enable backwards compatibility for profile plots after RELEASE 3.23

[tonywu1999]

Motivation and Context

#193

A while back, we added the "LABEL" column to ProteinLevelData to account for the protein turnover use case where there would be heavy-labeled summaries and light-labeled summaries. However, old saved datasets became incompatible for processing as a result with dataProcessPlots with profile plots.

Changes

• Account for edge case where LABEL is missing
• Remove warning related to aes + size parameter

Testing

Please describe any unit tests you added or modified to verify your changes.

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

Motivation and solution

Older saved datasets may not contain LABEL in ProteinLevelData. The plot-processing code now uses "Endogenous" as the label for run-summary data when LABEL is absent. The profile plot also uses a fixed line width, avoiding the size aesthetic mapping for lines.

Changes

• In .plotProfile, map the run-summary LABEL through raw_label_map when the summarized data contains LABEL; otherwise, use "Endogenous".
• In .makeSummaryProfilePlot, remove the line-level mapping from size to analysis and set geom_line(linewidth = 0.5). The point layers retain their existing size mapping.

Unit tests

• No tests are described in the supplied PR context.
• The repository contains tests/tinytest.R, but the available evidence does not show that this change adds or modifies tests.
• Test execution results were not provided.

Coding guidelines

• No current coding guideline review findings were provided, so guideline violations are unavailable.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 57cfa649-f341-4f74-84a3-68e64f198c2f

📥 Commits

Reviewing files that changed from the base of the PR and between d32ad97 and d8925cf.

📒 Files selected for processing (2)

• R/dataProcessPlots.R
• R/utils_dataprocess_plots.R

Included review availability: Your plan provides up to 2 included reviews per hour; 1 remains after this review.

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📝 Walkthrough

Walkthrough

The profile plot code now assigns a default label when summarized data lacks a LABEL column. It also uses a fixed line width while retaining analysis-based sizing for points.

Changes

Profile Plot Adjustments

Layer / File(s)	Summary
Conditional label assignment R/dataProcessPlots.R	When the summarized data has no LABEL column, the run-summary quant block assigns "Endogenous"; otherwise, it maps labels through raw_label_map.
Fixed profile line width R/utils_dataprocess_plots.R	The base plot mapping no longer ties line size to analysis. The line uses a fixed width, while point layers retain analysis-based sizing.

Estimated code review effort: 2 (Simple) | ~8 minutes

Merge Risk: ⚪ Minimal · up to d8925

Legacy profile inputs retain the endogenous label, and the fixed line width is compatible with the supported ggplot2 version. No material merge risk remains.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly identifies the profile-plot compatibility change and references the relevant release context.
Description check	✅ Passed	The description explains the motivation, lists the two changes, includes the required checklist, and identifies the related pull request. The Testing section does not document any tests, but the descr…
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
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.

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_{A rabbit checks the labels in the plot,
Adds “Endogenous” when one is not.
The lines stay steady, slim, and neat,
The points keep sizes tied to each analysis sheet.
Then hops away through data bright.}

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

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