ggpubr Files

New features

• Added outliers parameter to ggboxplot() to control the display of outlier points. Set outliers = FALSE to remove the black dots representing outliers from box plots (#614, @hswl1314).

Minor changes

• Enhanced automatic conversion of deprecated dot-dot notation (..p.signif.., ..eq.label..) to modern after_stat() calls with proper namespace qualification.
• Enhanced ggline() parameter handling for ggplot2 3.4.0+ compatibility:
  • Added linewidth parameter for line width
  • Deprecated size parameter for lines with helpful warning message
  • Maintained backward compatibility with existing size parameter
  • Prevents conflicts when both parameters are specified

Bug fixes

• Fixed namespace resolution issues with after_stat() calls that were causing failures in reverse dependency packages (bSi, PopComm). The convert_label_dotdot_notation_to_after_stat() function now properly handles namespace qualification while maintaining backward compatibility (#638).
• Improved evaluation environment setup to ensure ggplot2::after_stat() is accessible during plot building, resolving "could not find function after_stat" errors in downstream packages.
• Fixed equation format in stat_regline_equation() to display in standard mathematical convention "y = mx + b" instead of "y = b + mx" (#559, @tshates, @mwaak).
• Fixed compatibility with ggplot2 4.0.0. Updated gghistogram() tests to handle changes in binning standardization introduced in ggplot2 4.0.0 (#635, @teunbrand).
• Fixed stat_pvalue_manual() failing when fill or other aesthetics are provided in the parent ggplot layer. The function now sets inherit.aes = FALSE by default to prevent conflicts between parent plot aesthetics and the p-value annotation data (#621, @fncokg).
• Fixed deprecation warnings for newer package versions:
• Replaced deprecated ggplot2::is.ggplot() with ggplot2::is_ggplot() in ggpar()
• Updated .data$column syntax to quoted column names in geom_pwc() for tidyselect 1.2.0+ compatibility
• Added all_of() wrapper in unnest() utility function for tidyselect compatibility
• Replaced the option size by linewidth in ggplot2 element_line() and element_trect() functions.
• Fixed deprecation warning in stat_regline_equation() by automatically converting deprecated dot-dot notation (..eq.label.., ..adj.rr.label.., ..p.signif.., etc.) to after_stat() syntax for ggplot2 3.4.0+ compatibility (#623, @hinkyisme).
• Fixed deprecation warnings in add_summary() and ggerrorplot() for ggplot2 compatibility:
  • Updated internal stat_summary() parameters to use fun, fun.min, and fun.max instead of deprecated fun.y, fun.ymin, and fun.ymax (#587, @vlonde).
  • Fixed line aesthetic parameters by using linewidth instead of size for line-based error plots