fix: volcano summary feature handling and layout

[phoman14]

Changes

• Fix plot_volcano_summary() to respect non-Gene feature ID columns.
• Delegate volcano summary plotting to plot_volcano_enhanced() so individual EnhancedVolcano plots are stitched into a grid.
• Scale saved volcano summary output dimensions by grid rows/columns so each stitched plot keeps its single-plot proportions.
• Add separate axis tick label sizing and align volcano legend significance labels with the y-axis (p-value versus FDR).
• Update NEWS.md for PR fix: volcano summary feature handling and layout #239.

Issues

No linked issue.

PR Checklist

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write unit tests for any new features, bug fixes, or other code changes.
• Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
• Update NEWS.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
• Run devtools::check() locally and fix all notes, warnings, and errors.

[Copilot]

Pull request overview

This PR updates MOSuite’s volcano summary plotting so it correctly supports non-Gene feature ID columns, and switches the summary plot rendering to reuse the existing plot_volcano_enhanced() implementation (stitching multiple EnhancedVolcano plots into a grid with appropriately scaled output dimensions and updated axis/legend labeling).

Changes:

• Add a regression test ensuring plot_volcano_summary() respects a non-Gene feature ID column.
• Refactor plot_volcano_summary() to delegate plotting to plot_volcano_enhanced() (grid stitching + scaled output size).
• Extend plot_volcano_enhanced() with tick-label sizing, improved legend labels (p-value vs FDR), and configurable grid layout scaling; update NEWS.md and Rd files accordingly.

Reviewed changes

Copilot reviewed 4 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/testthat/test-plot_volcano_summary.R	Adds coverage for non-Gene feature ID column handling.
R/plot_volcano_summary.R	Delegates summary plotting to plot_volcano_enhanced() and threads new axis sizing params.
R/plot_volcano_enhanced.R	Adds tick label sizing, legend label alignment, and grid-aware output dimension scaling.
NEWS.md	Adds a user-facing entry for the volcano summary fixes.
man/plot_volcano_summary.Rd	Documents new axis label/tick sizing parameters.
man/plot_volcano_enhanced.Rd	Documents new tick sizing and grid layout/output scaling parameters.

Files not reviewed (2)

• man/plot_volcano_enhanced.Rd: Generated file
• man/plot_volcano_summary.Rd: Generated file

[Copilot]

Pull request overview

Copilot reviewed 9 out of 11 changed files in this pull request and generated 3 comments.

Files not reviewed (2)

• man/plot_volcano_enhanced.Rd: Generated file
• man/plot_volcano_summary.Rd: Generated file

Comments suppressed due to low confidence (3)

R/plot_volcano_summary.R:57

• plot_volcano_summary() is exported but aspect_ratio has been removed from the public signature. Any external caller (including internal tooling) still passing aspect_ratio will now error with an unused argument; the repo’s Galaxy metadata still references this parameter (inst/extdata/galaxy/0_nidap-1.0/missing_parameters.csv:12). Consider keeping aspect_ratio as a deprecated argument (even if ignored) or adding ... to allow older callers to continue working while they are updated.

    image_width = 15,
    image_height = 15,
    dpi = 300,
    use_default_grid_layout = TRUE,
    number_of_rows_in_grid_layout = 1,
    plot_filename = "volcano_summary.png",

inst/extdata/json_args/defaults/plot_volcano_enhanced.json:27

• The defaults JSON for plot_volcano_enhanced hasn’t been updated for newly added styling/grid parameters in the R function signature (e.g., axis_tick_lab_size, label colors, point/threshold colors, and grid layout controls). If this JSON is used for CLI/config defaults, those arguments will be unavailable and may be dropped during parsing.

  "axis_lab_size": 24,
  "point_size": 2,
  "image_width": 3000,

inst/extdata/json_args/common/plot_volcano_enhanced.json:27

• The common JSON args for plot_volcano_enhanced hasn’t been updated for newly added styling/grid parameters in the R function signature (e.g., axis_tick_lab_size, label colors, point/threshold colors, and grid layout controls). This can make these options unavailable/ignored when building configs from the common JSON.

  "axis_lab_size": 24,
  "point_size": 2,
  "image_width": 3000,

[codecov]

Codecov Report

❌ Patch coverage is 88.58859% with 38 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.82%. Comparing base (255bfb9) to head (eca71fd).

Files with missing lines	Patch %	Lines
R/plot_volcano_enhanced.R	81.12%	37 Missing ⚠️
R/plot_volcano_summary.R	99.08%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #239      +/-   ##
==========================================
+ Coverage   82.55%   83.82%   +1.27%     
==========================================
  Files          23       24       +1     
  Lines        4024     4137     +113     
==========================================
+ Hits         3322     3468     +146     
+ Misses        702      669      -33     

☔ View full report in Codecov by Harness.
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[kelly-sovacool]

A test is failing, looks like a snapshot just needs to be updated

https://github.com/CCBR/MOSuite/actions/runs/30355909218/job/90263993915?pr=239#step:5:1407

[phoman14]

A test is failing, looks like a snapshot just needs to be updated

https://github.com/CCBR/MOSuite/actions/runs/30355909218/job/90263993915?pr=239#step:5:1407

@kelly-sovacool so there are additional warnings when running on github, see below. Should i apply the changes highlighted in this message?

Condition
Warning:
Using size aesthetic for lines was deprecated in ggplot2 3.4.0.
i Please use linewidth instead.
i The deprecated feature was likely used in the EnhancedVolcano package.
Please report the issue to the authors.
Warning:
The size argument of element_line() is deprecated as of ggplot2 3.4.0.
i Please use the linewidth argument instead.
i The deprecated feature was likely used in the EnhancedVolcano package.
Please report the issue to the authors.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 13 changed files in this pull request and generated no new comments.

Files not reviewed (3)

• man/plot_venn_diagram.Rd: Generated file
• man/plot_volcano_enhanced.Rd: Generated file
• man/plot_volcano_summary.Rd: Generated file

Comments suppressed due to low confidence (2)

R/plot_volcano_enhanced.R:357

• When label_significant_features_only filters out most/all rows, df_sub[1:num_features_to_label, ...] can return NA labels (or even NA-filled rows). Those NA values then flow into genes_to_label/selectLab and can produce incorrect labeling behavior or warnings/errors. Guard against empty df_sub and explicitly drop NA/empty labels before calling EnhancedVolcano().

    if (label_significant_features_only) {
      df_sub <- df[
        df[[sig_name]] <= signif_threshold &
          abs(df[[lfc_name]]) >= change_threshold,
      ]
    } else {
      df_sub <- df
    }

    genes_to_label <- as.character(df_sub[1:num_features_to_label, label_col])
    split_values <- unlist(strsplit(gsub(",", " ", custom_gene_list), " "))

man/plot_venn_diagram.Rd:184

• The plot_filename documentation here claims that when multiple comparisons are saved separately, the comparison name is appended to the filename. plot_venn_diagram() only saves a single output plot and does not implement per-comparison filename suffixing, so this sentence is misleading and should be removed for this function.

[kelly-sovacool]

There was a bug in plot_volcano_enhanced where it was only plotting two contrasts instead of all three. I fixed it in 92333bd. @phoman14 take a look and let me know what you think!