fix(anomaly-metrics): Fix plotting x-axis for anomaly metrics

[tonywu1999]

PR Type

Bug fix, Documentation

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Description

• Use numeric run-order x-axis

• Reduce clutter from long run names

• Refresh generated documentation metadata

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Diagram Walkthrough

flowchart LR
  A["Quality metrics data"]
  B["Run factor levels"]
  C["Numeric run positions"]
  D["Cleaner x-axis plot"]
  A -- "derive order from" --> B
  B -- "map runs to" --> C
  C -- "render as" --> D

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File Walkthrough

	Relevant files
Configuration changes	DESCRIPTION Update roxygen configuration metadata                                        DESCRIPTION Adds Config/roxygen2/version: 8.0.0. Updates package documentation-generation metadata. +1/-1
Bug fix	plot_quality_metrics.R Plot metrics against numeric run order                                      R/plot_quality_metrics.R Documents numeric run-order positions on the x-axis. Maps Run factor levels to RunOrder. Uses continuous x-axis breaks every five runs. Renames x-axis label to Run order. +14/-9
Documentation	utils_documentation.R Refresh shared import documentation formatting                      R/utils_documentation.R Consolidates MSstatsConvert import documentation onto one line. Keeps the same imported functions while refreshing roxygen formatting. +1/-2      MSstatsQualityMetricsPlot.Rd Document numeric x-axis behavior                                                  man/MSstatsQualityMetricsPlot.Rd Updates details for the numeric run-order x-axis. Explains run positions derive from Run factor levels. Clarifies behavior with and without runOrder. +6/-4      reexports.Rd Update generated reexport link syntax                                        man/reexports.Rd Updates MSstatsConvert reexport links to qualified Rd syntax. Adds function-style link labels with parentheses. +1/-1

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 52b5a193-8d72-4fba-9f33-944a80bda151

📥 Commits

Reviewing files that changed from the base of the PR and between 3fa0bd1 and 9071125.

📒 Files selected for processing (5)

• DESCRIPTION
• R/plot_quality_metrics.R
• R/utils_documentation.R
• man/MSstatsQualityMetricsPlot.Rd
• man/reexports.Rd

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix-quality-plots

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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 Possible Issue scale_x_continuous(breaks = seq(5, length(run_levels), by = 5)) fails when there are fewer than 5 run levels because seq(5, 1..4, by = 5) has the wrong step direction. This makes plotting error for small datasets instead of returning a plot. Consider guarding this case or generating breaks from 1 upward. scale_x_continuous(breaks = seq(5, length(run_levels), by = 5)) +

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Handle non-factor run columns levels(input_df$Run) returns NULL when Run is not already a factor, causing RunOrder to become all NA and the plot to fail or render incorrectly. Add a fallback that matches the documented alphabetical ordering for non-factor runs. R/plot_quality_metrics.R [103-104] -run_levels <- levels(input_df$Run) +run_levels <- if (is.factor(input_df$Run)) { + levels(input_df$Run) +} else { + sort(unique(as.character(input_df$Run))) +} plot_df$RunOrder <- match(as.character(plot_df$Run), run_levels) Suggestion importance[1-10]: 8 __ Why: This correctly identifies that levels(input_df$Run) can be NULL for non-factor Run values, causing RunOrder to become NA and breaking or emptying the plot. The fallback to sorted unique run names matches the documented alphabetical behavior.	Medium
	Fix small-run plotting failure seq(5, length(run_levels), by = 5) errors when there are fewer than five runs because the sequence direction conflicts with the positive step. Use a guarded break calculation so small datasets still plot successfully. R/plot_quality_metrics.R [113] -scale_x_continuous(breaks = seq(5, length(run_levels), by = 5)) + +scale_x_continuous( + breaks = if (length(run_levels) <= 5) { + seq_along(run_levels) + } else { + unique(c(1, seq(5, length(run_levels), by = 5))) + } +) + Suggestion importance[1-10]: 8 __ Why: This is a valid bug fix because seq(5, length(run_levels), by = 5) errors when there are fewer than five runs. The guarded break calculation preserves plotting for small datasets while keeping periodic breaks for larger ones.	Medium