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ggplot2 v4.0.0 Known Issues in Seurat

Overview

ggplot2 version 4.0.0 (released September 2025) introduced breaking changes by migrating from S3 to S7 object system. This document tracks known compatibility issues and their status.

Fixed Issues

1. DarkTheme() - Deprecated size parameter ✅

Status: FIXED
Files: R/visualization.R (lines 6433-6445)
Changes:

  • Replaced element_rect(fill = 'black', size = 0) with linewidth = 0
  • Replaced element_line(colour = 'white', size = 1) with linewidth = 1
  • Replaced element_line(size = 0) with linewidth = 0

2. LabelClusters() - S7 object color retrieval ✅

Status: FIXED
Issues: #10156, #10176
Files: R/visualization.R (lines 6134-6227)
Problem: With S7 objects, pb$data returns numeric coordinates instead of valid colors
Solution: Extract colors directly from plot scales using pb$plot$scales$get_scales() Changes:

  • Added color scale extraction from plot scales
  • Created group_colors mapping with validation
  • Fixed data.medians$color assignment to use explicit group_colors mapping

Outstanding Issues (Require ggplot2 Package Fix)

3. VlnPlot - S4SXP Error 🔴

Status: NEEDS GGPLOT2 FIX
Issues: #10101, #10188, #10160
Files: Not Seurat-specific code
Error:

Error in deparse(substitute(e2, env = caller_env(2))) :
'S4SXP': should not happen - please report

Root Cause: Deep incompatibility between ggplot2 v4 S7 objects and R's substitute() function calls within ggplot2 internals
Workaround: Downgrade to ggplot2 3.5.2

remotes::install_version("ggplot2", version = "3.5.2", repos = "https://cran.r-project.org")

Note: Some packages (e.g., clusterProfiler >= 4.12.0) require ggplot2 >= 4.0.0, creating dependency conflicts

Potential Issues (To Monitor)

4. ggplot_build()$plot$data Access Pattern ⚠️

Status: MONITORING
Files: R/visualization.R (lines 5948, 7795)
Functions: GGpointToPlotly(), GGpointToPlotlyBuild()
Concern: Direct $plot$data access may behave differently with S7 objects
Impact: Unknown - needs testing with real-world usage

5. plot$layers Access Pattern ⚠️

Status: MONITORING
Files: R/visualization.R (multiple locations)
Concern: plot$layers[[i]]$data and plot$layers[[i]]$mapping access may need S7 updates
Impact: Unknown - backward compatibility should handle this, but monitor for issues

Migration Notes

What Changed in ggplot2 v4

  • S7 Object System: ggplot objects now use S7 instead of S3
  • Deprecated Parameters:
    • size → linewidth in element_rect() and element_line()
    • Keep size in element_text() (NOT deprecated)
  • S7 Backward Compatibility: $data and $layers access still works, but internal data structures changed
  • New Features:
    • Theme improvements (ink/paper/accent, palette., theme_sub_)
    • geom_label() new aesthetics (linewidth, border.colour, text.colour)

Testing Recommendations

  1. Test all visualization functions with ggplot2 v4
  2. Verify label.box functionality in DimPlot variants
  3. Check VlnPlot alternatives if S4SXP persists
  4. Monitor Plotly integration functions for S7 issues

Dependencies

  • Minimum ggplot2 version: 3.5.2 (for compatibility)
  • Target ggplot2 version: 4.0.0+ (once S4SXP issue resolved upstream)

References

Last Updated

2025-11-27