fix(profile-plot): Fix summaries for profile plots for protein turnover

[tonywu1999]

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PR Type

Bug fix

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Description

• Fix summary labels in profile plots

• Map raw labels by labeling mode

• Support turnover and heavy/light outputs

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Diagram Walkthrough

flowchart LR
  p["Processed labels"] -- "derive" --> m["Raw label map"]
  s["Summarized run data"] -- "apply mapped LABEL" --> q["Correct profile plot summaries"]
  m -- "used by" --> q

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File Walkthrough

	Relevant files
Bug fix	dataProcessPlots.R Correct summary label mapping in profile plots                      R/dataProcessPlots.R Add raw_label_map for each label mode Map H/L to displayed summary labels Replace fixed summary label selection Fix run summaries for turnover plots +7/-4

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

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Run ID: 66019f94-222b-41fd-a1cf-0197e31413ab

📥 Commits

Reviewing files that changed from the base of the PR and between 8ebaa57 and 9dd21b0.

📒 Files selected for processing (1)

• R/dataProcessPlots.R

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix-profile-2

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[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Runtime error The new run-summary path now requires summarized to have a LABEL column. The previous implementation worked without that field by assigning a constant summary label, but this lookup will fail with object 'LABEL' not found for summary tables that are only keyed by protein/run, such as label-free or single-label outputs. single_protein_summ = summarized[Protein == all_proteins[i], ] quant = single_protein_summ[ Protein == all_proteins[i], list(PROTEIN = unique(Protein), PEPTIDE = "Run summary", TRANSITION = "Run summary", FEATURE = "Run summary", LABEL = raw_label_map[LABEL], RUN = RUN, ABUNDANCE = LogIntensities, FRACTION = 1, Wrong mapping raw_label_map[LABEL] is unsafe when LABEL is a factor, because R subsets named vectors by the factor's underlying integer codes rather than its displayed values. If the factor levels are ordered differently from H, L, the summary traces can be mislabeled (for example, H becoming Light). Converting LABEL to character before indexing avoids this. LABEL = raw_label_map[LABEL], RUN = RUN,

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix factor-based lookup LABEL is often a factor in data.table, and indexing a named vector with a factor uses the underlying integer codes instead of the label text. That can silently assign the wrong summary label when the factor levels are reordered or reduced. Convert LABEL to character before looking it up in raw_label_map. R/dataProcessPlots.R [392] -LABEL = raw_label_map[LABEL], RUN = RUN, +LABEL = unname(raw_label_map[as.character(LABEL)]), RUN = RUN, Suggestion importance[1-10]: 8 __ Why: This is a valid correctness issue: if summarized$LABEL is a factor, raw_label_map[LABEL] can index by the factor's internal integer codes instead of its text values. Converting LABEL with as.character() makes the lookup reliable and prevents silently wrong labels in the summary plot.	Medium
	Preserve unmapped label values The new mapping assumes every summary LABEL is a raw H/L code, but rows that already contain normalized values like Heavy, Light, Reference, or Endogenous will become NA. Preserve the original label when no entry exists in raw_label_map so the summary rows are still plotted correctly. R/dataProcessPlots.R [392] -LABEL = raw_label_map[LABEL], RUN = RUN, +LABEL = { + mapped_label <- unname(raw_label_map[as.character(LABEL)]) + ifelse(is.na(mapped_label), as.character(LABEL), mapped_label) +}, RUN = RUN, Suggestion importance[1-10]: 7 __ Why: This is a reasonable robustness fix because raw_label_map only defines raw H/L keys, so already-normalized values in LABEL would otherwise become NA. Falling back to the original LABEL preserves plotting behavior without changing the mapped case.	Medium