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Changelog

Source: NEWS.md

ggpubr 1.0.0.9000

ggpubr 1.0.0

CRAN release: 2026-07-06

New features

New functions

New arguments, computed variables, and input support

  • ggmaplot() gains an optional facet.by argument to split the MA plot into multiple panels (e.g. one per contrast or species). Top genes are selected per panel, while point colors use the same significance thresholds in every panel. Default output (no facet.by) is unchanged (#498).

  • stat_cor() and stat_regline_equation() gain a label.anchor argument. With label.anchor = "panel" the label is placed at the true panel-relative position (npc), so labels stay aligned across panels or facets whose axis ranges differ - e.g. facet_wrap(scales = "free_y"), geom_smooth() extending each panel by a different amount, or separate plots combined with ggarrange(). The default label.anchor = "data" keeps the previous data-range placement, so existing plots are unchanged (#248).

  • geom_bracket() gains an orientation argument. orientation = "vertical" draws a native vertical bracket (the bar spans the y axis, the tips point left and the label is rotated), specified with ymin/ymax/x.position — useful to annotate plots where the comparison runs along the y axis, e.g. Kaplan-Meier curves (it is designed for a continuous x axis). The default orientation = "horizontal" is unchanged, and it cannot be combined with coord.flip = TRUE (#456).

  • ggpaired() gains an opt-in jitter argument that spreads the paired points horizontally to reduce overlap. Each subject (id) gets a single offset, so its two points move together and the connecting line stays intact, and only the horizontal positions change (the values are never moved). Default jitter = 0 leaves the plot unchanged (#407).

  • ggboxplot(), ggviolin() and ggstripchart() gain an opt-in show.n argument. When show.n = TRUE, the number of observations ("n = <count>") is displayed at the top of each group. When the groups are dodged (a color/fill grouping with a dodging position), one count is shown per group; otherwise a single count is shown per x-axis tick. Counts respect select/remove and are computed per facet. Default is show.n = FALSE, so existing plots are unchanged (#598, #627).

  • ggarrange() gains a spacing argument to increase the gap between the arranged plots (a long-requested option). It adds a uniform margin, in text-line units, around each plot. Default is 0 (no extra space; each plot keeps its own margins, so existing arrangements are unchanged) (#151).

  • compare_means() gains an id argument for paired comparisons. Without it, a paired test (paired = TRUE) pairs observations by row order, so the p-value is wrong when the data are not sorted so that the compared groups align by subject. Passing id (the name of a subject-identifier column) pairs the observations by id instead — row-order independent, using only the complete pairs (via rstatix, so the result matches a direct rstatix::t_test()/wilcox_test() call). It works for a two-group, a pairwise (more than two groups) and a ref.group comparison with t.test/wilcox.test. Default (id = NULL) is unchanged (#560).

  • stat_compare_means() also gains the id argument, so a paired test can be aligned by subject id directly on a plot (e.g. ggpaired(...) + stat_compare_means(paired = TRUE, id = "subject")), displaying the correct p-value even when the data are not sorted by subject. Plots without id are unchanged (#560).

  • geom_pwc() and stat_pwc() gain a p.adjust.n argument giving the number of comparisons to use for the p-value adjustment (passed as n to stats::p.adjust()). Default is NULL (adjust by the number of computed p-values, unchanged behavior); set it when the displayed comparisons are a subset of a larger family so the adjustment reflects that larger size. It must be at least the number of p-values being adjusted, and applies to the panel-level adjustment (p.adjust.by = "panel") and the single-comparison case (#612).

  • annotate_figure() gains column.titles and row.titles arguments to add a title above each column and to the left of each row of an arranged grid (useful for publication panels). Each accepts a character vector (one title per column / per row, rendered in bold) or a list of grobs (e.g. built with text_grob()) for full styling control; row.titles are rotated 90 degrees. The titles are placed in reserved space (they do not overlap the plots) and are evenly spaced, so they assume equal-sized columns / rows (the ggarrange() default). Default is NULL (no titles; existing figures are unchanged) (#573).

  • ggbarplot() gains a numeric.x.axis argument (already available in ggline() and ggerrorplot()). With numeric.x.axis = TRUE the x variable is kept numeric instead of being coerced to a discrete factor, so bars are drawn at their numeric x positions (e.g. a time axis). Default is FALSE (unchanged behavior) (#463).

  • geom_bracket() and stat_pvalue_manual() gain a tip.length.ref argument controlling what tip.length is a fraction of. With the default tip.length.ref = "data" the tips are a fraction of the data range (unchanged behavior). With tip.length.ref = "axis" the tips are a fraction of the y-axis range (ylim/scale_y_*), which renders at the same physical fraction across plots and therefore gives visually constant tip lengths regardless of the data range - useful to keep tips consistent across facets or across separate plots with different scales (#362). stat_compare_means(comparisons =) draws its brackets via ggsignif::geom_signif() and does not support tip.length.ref; passing it there now emits an informative message pointing to stat_pvalue_manual(..., tip.length.ref = "axis") instead of being silently ignored (#362).

  • stat_cor() and stat_regline_equation() gain a label.y.step argument giving the vertical spacing (in text-line units) between the labels of successive groups. Default is 1.4 (unchanged behavior). Setting label.y.step = 0 stops the per-group vertical shift so labels align across facet panels when a factor is mapped to an aesthetic that also defines the facets (the long-standing “labels climbing stairs across facets” behavior; #248). This control was inspired by the vstep argument in the ggpmisc package (by Pedro J. Aphalo), from which ggpubr’s correlation/regression label-positioning logic was originally adapted; this is acknowledged via @seealso in ?stat_cor.

  • ggviolin() gains a drop argument (passed to ggplot2::geom_violin()), default TRUE (unchanged behavior). Previously the argument was silently dropped, so grouped violins where a sub-sample has too few points to draw a density (which geom_violin() removes, including from the dodge position) could not be kept aligned with added boxplots / dot plots. Setting drop = FALSE together with position = position_dodge(0.8, preserve = "single") now reserves the empty dodge lane so all geoms stay aligned (#381).

  • ggarrange() gained the ability to choose which plot(s) supply the shared legend: common.legend now also accepts one or several plot indices. common.legend = 2 uses the second plot’s legend (handy when the first plot’s legend is not representative, e.g. a group is missing in the first plot), and common.legend = c(1, 2) keeps and combines the legends of the listed plots into a single shared block (side by side for legend = "top"/"bottom", stacked for "left"/"right") - useful when the arranged plots genuinely need different legends. The documentation of common.legend was also clarified: common.legend = TRUE keeps the first plot’s legend (it does not merge or validate legends), so plots should share a consistent scale for a single shared legend to be correct. Logical TRUE/FALSE behave exactly as before (#347).

  • ggdonutchart() gained a label.repel argument (default FALSE). When TRUE, slice labels are placed with ggrepel::geom_text_repel() and connected to their slice with leader lines, so the labels of many small slices no longer overlap (or get dropped). The default output is unchanged (#655).

  • ggboxplot() now accepts a position argument (e.g. position = position_dodge(0.9)), like ggviolin()/ggdotplot() already do. Previously passing position errored (formal argument "position" matched by multiple actual arguments) because the dodge was hardcoded; the default is unchanged (position_dodge(0.8)), so grouped box plots look the same unless you set it (#615).

  • ggsummarytable() gains an angle argument to rotate the summary-table text; default (angle = 0) is unchanged (#595).

  • ggmaplot() gains a line.color argument to set the threshold line color; default (“black”) is unchanged (#322).

  • ggarrange() gains a byrow argument (default TRUE) to fill the plot grid by column (byrow = FALSE) instead of by row; forwarded to cowplot::plot_grid() (#225).

  • stat_regline_equation() gains coef.digits and rr.digits arguments to control the number of significant digits shown for the regression-equation coefficients and R2; defaults (2) reproduce the previous output (#312).

  • Added formatting parameters to statistical helpers:

    • p.format.style
    • p.digits
    • p.leading.zero
    • p.min.threshold
    • p.decimal.mark

  • Added p.format.signif support and related label handling paths.

  • stat_pvalue_manual() gains a p.digits argument (default 3) that formats numeric p-value label columns for display (e.g. label = "p" or label = "p.adj"), using the same format_p_value() engine as stat_anova_test(). This restores clean labels (e.g. 0.0156 instead of 0.015625) with rstatix >= 1.0.0, which now returns full-precision pairwise p-values. Character labels (significance symbols, pre-formatted strings, glue expressions) are unaffected. Set p.digits = NULL to print the raw value.

  • stat_pvalue_manual() additionally gains p.format.style, p.leading.zero, p.min.threshold and p.decimal.mark, matching the p-value formatting arguments already available in stat_compare_means(), geom_pwc() and stat_anova_test(). These are opt-in and default so that the rendered labels are unchanged; for example p.min.threshold = 0.001 displays very small p-values as < 0.001, and p.format.style = "nejm" applies a journal style.

  • stat_cor() gains two label-formatting arguments:

    • r.leading.zero — set to FALSE to drop the leading zero of the correlation coefficient (e.g. .73 instead of 0.73), completing APA-style reporting together with p.leading.zero (#540). The dropped leading zero is preserved through plotmath rendering (the value is quoted so it is not silently re-normalized back to 0.73 in the default expression output).
    • p.coef.name — symbol for the p-value label; use "P" for an uppercase p-value (#541).

  • stat_cor() exposes two new computed variables, rmse and rmse.label, for the root mean square deviation (RMSE/RMSD) between x and y — useful for reporting agreement between paired measurements on the same scale (e.g. predicted vs. reference values). Display it with aes(label = after_stat(rmse.label)), or combine it with the correlation coefficient using paste(). The default label is unchanged (#458).

  • stat_cor() can now display the confidence interval of the correlation coefficient, via the new computed variables conf.int.low, conf.int.high and conf.int.label (e.g. "95% CI [0.21, 0.75]") and a conf.level argument (default 0.95). Show it with aes(label = after_stat(conf.int.label)), or combine it with the coefficient using paste(). The confidence interval is available for method = "pearson" only; it is NA for Spearman/Kendall. The default label is unchanged (#418).

Main changes

Compatibility

  • Added compatibility updates for modern ggplot2, dplyr, and tidyr.
  • Updated legacy size usage to linewidth where required by recent ggplot2.
  • Completed the size -> linewidth migration for the remaining line layers that still passed the deprecated size argument: the mean/median reference line added by gghistogram(add = ...) and ggdensity(add = ...), and the connector segments of ggdotchart(add = "segments"). These no longer emit ggplot2’s “size aesthetic for lines was deprecated” or “Ignoring empty aesthetic: size” warnings, and the requested line width is now applied via linewidth.
  • ggmaplot() no longer emits an “Ignoring empty aesthetic: size” warning on its default call; the point layer sets size only when the user supplies a value.
  • Replaced deprecated tidyverse APIs in affected helper functions.
  • Added package startup lock-file checks and clean_lock_files() helper.
  • Relaxed minimum ggrepel dependency to >= 0.9.2 to keep Ubuntu oldrel (R 4.4.x) CI dependency resolution working.
  • geom_pwc() now detects an absent ref.group in a grouped subset via the rstatix_missing_ref_group condition class raised by recent rstatix (walking the parent chain with rlang::cnd_inherits()), in addition to matching the error message. This keeps the “skip ref-less subsets” behaviour working after rstatix made that error message clearer (rstatix #153); older rstatix versions are still handled via the message fallback.
  • The minimum required rstatix version is now >= 1.0.0 (the version that introduced the id argument used by compare_means(id = ), and the full-precision pairwise p-values relied on by the p-value formatting).

Validation and messaging

  • Hardened sparse-group handling in stat_compare_means() and geom_pwc().
  • Non-comparable grouped subsets (insufficient levels/observations) are now skipped while preserving valid inferential comparisons in the same layer.
  • Added per-group skip diagnostics in geom_pwc() so users can see which grouped subsets were skipped and why (e.g., missing ref.group or insufficient levels).
  • Added regression tests for mixed comparable/non-comparable subsets and fully sparse subsets.
  • Passing ggtheme = NULL to the plotting functions (e.g. ggscatter(), ggboxplot(), ggline(), gghistogram(), …) now skips applying a ggpubr theme, so the plot keeps ggplot2’s default theme or the theme set globally with theme_set(). Previously an explicit ggtheme = NULL was treated like an unset argument and theme_pubr() was still applied. Calls that omit ggtheme or pass a specific theme are unchanged (#561).
  • compare_means() now adjusts p-values within each group.by level (and response) rather than pooling all groups together, so a grouped adjustment matches filtering to one group and adjusting there. This changes p.adj values for calls that use group.by; ungrouped calls are unchanged (#200).
  • stat_compare_means(comparisons = ) now emits a one-time message (and the docs note) clarifying that the displayed pairwise p-values are not adjusted for multiple comparisons, pointing to geom_pwc() / stat_pvalue_manual() + compare_means(p.adjust.method = ) for corrected p-values (#293).

Documentation

  • Documented a recipe for labelling groups with significance letters (compact letter display): compute the pairwise comparisons and derive the letters with rstatix::add_cld(), then place them with geom_text() (see the “Significance letters” section in ?compare_means). Also covers the per-control letters case (a = differs from control 1, b = differs from control 2) (#464, #434).
  • Documented that a summarized ggbarplot() (e.g. add = "mean_se") must be faceted with the facet.by= argument, not by appending + facet_wrap()/+ facet_grid(): the summaries are pre-computed over facet.by, so a manually added facet pools the bars (and, for stacked bars, the error bars) across all panels (#739).
  • Clarified documentation to match existing behavior: the ggtheme default per function, the p-value threshold/precision defaults, the stat_compare_means() label separator (test method name, not correlation coefficient), and the package Description’s list of p-value formatting styles. Thanks to @erdeyl (#749).
  • Expanded test coverage for formatting helpers and compatibility paths.
  • Regenerated manuals and package documentation after source sync.
  • Closes #663 (stat_compare_means() fatal warning/error in sparse grouped subsets with modern tidyr).
  • Closes #334 (stat_compare_means(label = "p.format") rounding and formatting control).
  • Related: #540, #626.

Credits

Minor changes

  • Fixed ColorBrewer sequential palette parsing in .get_brewer_pal() so "YlOrBr" is recognized correctly.
  • Updated ggexport() to respect verbose = FALSE by suppressing filename print() output in multi-file raster/vector exports.
  • Hardened format_p_value() by validating non-NULL p.min.threshold as a single positive finite number.
  • Updated create_p_label() to preserve NA values in p.format (returning NA_character_ instead of stringifying to "p = NA").
  • theme_pubr() now draws the axis tick marks in black with linewidth 0.5, matching the axis lines; previously the ticks inherited a lighter grey/thinner style, visibly inconsistent when zoomed (#668).
  • theme_pubr() now sets strip.clip = "off" so the facet strip background border renders at its full linewidth. With the ggplot2 (>= 3.5.0) default (strip.clip = "on") the border was clipped to the strip area, cutting the outer half of the stroke so it looked thinner and misaligned with the panel when zoomed (follow-up to #668). Note: a facet label wider than its panel now overflows the strip instead of being truncated; restore clipping with + theme(strip.clip = "on") if needed.
  • xticks.by/yticks.by now anchor the axis breaks to round multiples of the step (e.g. 0, 100, 200) instead of the slightly-negative expanded axis minimum, which produced odd labels such as -20, 80, 180 on bar plots with ylim = c(0, 400) (#313).
  • Import the %||% operator from rlang; it is used in geom_bracket() and geom_pwc() but base R only provides it since R 4.4, so it could be unresolved on the R (>= 4.1) versions the package supports (#665).

Bug fixes

  • stat_welch_anova_test(label = "as_detailed_italic") and stat_welch_anova_test(label = "as_detailed_expression") now display the numeric F statistic instead of FALSE. Thanks to @erdeyl (#749).
  • ggbarplot() now supports mapping alpha to a discrete grouping variable together with a summary (e.g. alpha = clarity, add = "mean_ci", position = position_dodge()). Previously this errored at draw time ("alpha * 255": non-numeric argument to binary operator). The mean/CI is now computed per subgroup, the bars are faded per the alpha variable, and the error bars are dodged to stay aligned with their bars. Bar plots without an alpha grouping variable are unchanged (#404).
  • ggpar() no longer errors on ggsurvplot objects (or any plot whose theme uses ggtext::element_markdown(), e.g. survminer’s risk-table strata labels). Such markdown label elements are now left intact instead of triggering an “Only elements of the same class can be merged” error; output for all other plots is unchanged (#382).
  • geom_pwc() with an explicit list of comparisons no longer drops a whole facet/panel when a single requested pair cannot be tested (e.g. a group that is entirely NA or has fewer than two observations). The untestable comparison is skipped (with a message) and the remaining valid comparisons are still drawn (#542).
  • compare_means() and stat_compare_means() now forward extra test options (e.g. alternative = "greater") to the paired tests aligned by subject id, which were previously ignored on that path. Grouped and faceted paired-id comparisons also skip a subset that cannot be tested (fewer than two groups or no complete pairs) instead of failing the whole result/layer, while still reporting genuinely ambiguous data (e.g. duplicated ids). Thanks to @erdeyl (#732).
  • ggbarplot() now places the error bars of a stacked bar chart correctly when the data mix positive and negative values (e.g. above/below-ground measurements). The stacked error bars are cumulated per sign, matching position_stack(), so a negative segment’s error bar is drawn on its own side instead of being displaced to the other side (previously the misplacement also flipped with the factor-level order). Stacked charts with single-sign data are unchanged (#426).
  • ggviolin() now keeps grouped violins aligned with their added box/dot layers by default when a sub-group is too sparse for geom_violin() to compute a density (a single data point). Previously the sparse sub-group was dropped from the dodge, so the remaining violin re-centered and no longer lined up. When drop/position are left at their defaults and such a one-point grouped cell is present, the empty dodge lane is now reserved automatically. Balanced, ungrouped, faceted, and legitimately-unbalanced plots are unchanged, and an explicit drop/position still takes precedence (#381).
  • geom_bracket() (and stat_pvalue_manual()) now draw visible tips for a single bracket placed over a stat-computed y such as geom_bar()/geom_histogram(). Previously the bracket tips collapsed into a flat line because the y-axis range was trained only on the bracket’s single y.position; the tips are now sized against the fully-trained panel range at draw time, so they render correctly even with coord_cartesian(ylim = ...). Brackets with an already non-zero y range are unchanged (#631).
  • ggline() now dodges the jittered points together with the line and error bars. Previously, in a grouped line plot with add = "jitter" and position = position_dodge(), only the line and summary (e.g. mean_se) were dodged while the jittered points stayed centered, so they no longer sat under their group. The jitter now dodges by the same width. Plots without a position_dodge() (the default position = "identity") are unchanged (#436).
  • ggbarplot() now lines the error bars up with the bars when position = position_dodge2() is used. position_dodge2() places elements according to their own width, so the thin error bars did not sit on the centre of the wider bars they belong to (most visible with preserve = "single" when one x group has fewer bars than another). The error bars are now drawn at the actual bar positions. Other positions (identity, position_dodge(), position_stack()) are unchanged (#363).
  • geom_bracket() and stat_pvalue_manual() now place brackets correctly on a transformed y axis (e.g. scale_y_log10()). y.position is given in data units but was previously used directly in the scale’s transformed space, so brackets landed far off (e.g. at 10^30) and squashed the plot. The bracket y.position is now run through the scale’s transformation; on an untransformed (identity) scale this is a no-op, so existing plots are unchanged (#342).
  • The core plotting functions (ggscatter(), ggboxplot(), ggviolin(), ggline(), ggbarplot(), gghistogram(), ggdensity(), ggdotplot(), ggstripchart(), ggerrorplot(), ggecdf(), ggdotchart(), ggpaired(), ggqqplot()) now accept the British spelling colour as an alias for color. Previously colour was silently ignored (#317).
  • stat_regline_equation() now displays the correct equation for orthogonal polynomial fits such as formula = y ~ poly(x, 2). Previously the orthogonal basis coefficients were printed as if they were raw polynomial coefficients, giving a wrong equation that did not match the fitted curve. For a simple poly(x, k) term with an intercept, the equation is now computed from an equivalent raw = TRUE fit (identical curve, R², AIC, BIC). Linear, raw = TRUE, and I(x^2) formulas are unaffected; no-intercept models and transformed poly arguments (e.g. poly(log(x), 2)) keep their previous behavior (#653).
  • ggscatterhist() now aligns the marginal plots with the main scatter plot’s axes. The margins were built from the raw data, so anything that changed the scatter limits (ellipse = TRUE, position jitter, explicit xlim/ylim) left the marginal histograms/densities misaligned with the scatter. Each margin now inherits the scatter’s axis range (#220, #420).
  • geom_pwc() now places comparison brackets over the correct groups when an entire x-axis group has only NA values. Such a group is dropped before the statistical test runs; previously the surviving groups were renumbered from 1, which shifted the remaining brackets left. The bracket positions are now anchored to the discrete x scale so they stay aligned with the plotted groups (#575).
  • ggballoonplot() now honors user-supplied xlab/ylab instead of always blanking the axis titles; axis titles are still blank by default (#639).
  • ggpar(legend.title = ) now also titles size and alpha legends, not just colour/fill/linetype/shape (#412).
  • facet()/panel.labs: a NAMED panel.labs vector is now matched to the data levels by name, fixing mislabeled panels when the order differed; unnamed labels still map positionally (#643).
  • stat_compare_means() no longer fails with a “*.npc coord ...” error when a grouped x value is 0 (or negative); .group_coord() now guards against a non-positive group index and falls back to the first label coordinate (#594).
  • ggpar()/plot functions now apply xticks.by and yticks.by together; an internal else if previously dropped xticks.by whenever yticks.by was also supplied (#333).
  • stat_compare_means() now forwards the family argument to the comparison bracket labels; it was previously ignored whenever comparisons was set (#592, #624).
  • ggline() now supports two grouping variables at once (e.g. color and linetype, or an explicit group plus color); these are combined into a single interaction group so the right points are connected. Previously this errored with “the condition has length > 1” (#616, #375).
  • A NAMED palette vector no longer emits a spurious “No shared levels found between names(values) …” warning; the manual color/fill scale is now only applied to an aesthetic actually mapped in the plot. Unnamed palettes are unchanged, and a named palette whose names genuinely don’t match still warns (#642).
  • ggviolin() no longer crashes with scales = "free" (or "free_x"/"free_y"). The facet argument scales was being partial-matched to the violin scale parameter; it is now read with exact matching, so scales controls faceting and the violin scale keeps its default (#398).
  • xlim/ylim are now honored with orientation = "horizontal" (and rotate = TRUE). The limits are passed to coord_flip() instead of a separate coord_cartesian() that was silently replaced, which also removes the “Coordinate system already present” warning (#646).
  • ggpar() (and the plot functions) now honor legend.direction for all legend positions; it was previously ignored for legend = "top"/"bottom" (#652).
  • compare_means() no longer errors (“Can’t extract columns that don’t exist”) when a formula variable name contains a space (e.g. len ~ `spa ced`); the backticks that R adds to non-syntactic term names are now stripped before matching data columns (#385).
  • table_cell_font() and table_cell_bg() can now style an individual header cell (row = 1), not only body cells; they previously matched only the core-* grobs and silently did nothing for the header (#535).
  • ggmaplot() now draws the non-significant (“NS”) points behind the significant ones, so the up/down-regulated hits are no longer hidden under the grey NS cloud; the legend order (Up, Down, NS) is unchanged (#365).
  • ggboxplot() now forwards coef to geom_boxplot(), so coef = 0 can be used to omit the whiskers; it was previously dropped by geom_exec() (#517).
  • tab_add_title() / tab_add_footnote(): the just argument now actually positions the text — "center"/"right" anchor the title/footnote across the table width instead of around a fixed point — and the text is no longer clipped when it is wider than the table (#302).
  • annotate_figure(): the figure label (fig.lab) now uses a length-independent horizontal justification, so labels of different lengths keep the same anchor and captions align across figures; previously a longer label was shifted away from the corner (#185).

ggpubr 0.6.3

CRAN release: 2026-02-24

Major changes

  • Raised minimum R version to R >= 4.1.0 (from R >= 3.1.0) to match ggplot2 >= 3.5.2 requirement.
  • Raised minimum dplyr version to dplyr >= 1.1.0 (from dplyr >= 0.7.1) to use modern reframe(), slice_head(), slice_tail(), across(), and where() functions.

Minor changes

Bug fixes

ggpubr 0.6.2

CRAN release: 2025-10-17

Bug fixes

  • Fixed compatibility with R-devel r88748 (2025-08-31) which changed Wilcoxon test to provide exact conditional two-sample inference with ties. The compare_means() function now sets exact = FALSE for wilcox.test() and pairwise.wilcox.test() to maintain backward compatibility and consistent p-values across R versions (#647).

ggpubr 0.6.1

CRAN release: 2025-06-27

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_rect() 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

ggpubr 0.6.0

CRAN release: 2023-02-10

New features

Major changes

Minor changes

  • ggtexttable(): doc updated with another example; text justification for individual cells/rows/columns (#335).
  • ggpie(): setting the default of clip = "off" in coord_polar() so that ggpie() does not crop labels (#429)
  • as_ggplot(): using null_device to avoid blank page #306 and #158
  • ggarrange(): using null_device to avoid blank page #306 and #158
  • Indexing variable in a data frame: using df[[x]] instead of df[, x] to make sure that the result is a vector even if the df is a tibble.
  • ggexport(): support added for graphics device svg (#469)
  • ggpie() and ggdonutchart() now fully reacts to the option lab.font (#502)
  • Replacing deprecated gather_() in both internal (.check_data()) and exported functions (compare_means()) (#513)
  • stat_compare_means(): The dot-dot notation (..p.signif..) was deprecated in ggplot2 3.4.0; after_stat(p.signif) should be used; updated so that ..p.signif.. is automatically converted into after_stat() format without warning for backward compatibility.
  • Enable faceting by column names with spaces (#391)
  • Licence changed to GPL (>= 2) (#482)
  • desc_statby() doc updated to clarify the difference between SD (standard deviation) and SE (standard error) (#492)
  • The message geom_smooth() using formula 'y ~ x' is now turned off in ggscatter()(#488)

Bug fixes

  • ggtext(): fix warning “filter_() was deprecated in dplyr 0.7.0”.
  • ggqqplot(): the argument conf.int is taken into account now when specified (#524).
  • ggqqplot(): Fixing the warning: “The following aesthetics were dropped during statistical transformation: sample” (#523)
  • Requiring rstatix v >=0.7.1.999 for preserving factor class in emmeans_test() (#386)
  • ggmaplot(): Suppressing ggmaplot warning: Unlabeled data points (too many overlaps). Consider increasing max.overlaps (#520)
  • compare_means(): works now when the grouping variable levels contain the key words group2 or group1 (#450)
  • ggparagraph() : fixing bug about minimum paragraph length (#408)
  • ggexport(): the verbose argument is now considered when specified by user (#474)

ggpubr 0.5.0

CRAN release: 2022-11-16

New features

  • New functions stat_anova_test(), stat_kruskal_test(), stat_welch_anova_test(), stat_friedman_test() and geom_pwc() added. These are flexible functions to add p-values onto ggplot with more options. The function geom_pwc() is for adding pairwise comparisons p-values to a ggplot; supported statistical methods include “wilcox_test”, “t_test”, “sign_test”, “dunn_test”, “emmeans_test”, “tukey_hsd” and “games_howell_test”.
  • New functions to convert character vector coordinates into NPC (normalized parent coordinates) and data coordinates: as_npc(), npc_to_data_coordinates() and get_coord().
  • Global options:
    • New function ggpubr_options() to display allowed global options in ggpubr
    • New available package options: ggpubr.parse_aes. Logical indicating whether to parse aesthetic variable names. Default is TRUE. For example, if you want ggpubr to handle non-standard column names, like A-A, without parsing, then set this option to FALSE using options(ggpubr.parse_aes = FALSE).

Minor changes

  • Minimum rstatix version needed is set to 0.7.1
  • Minimum ggplot2 version needed is set to 3.4.0
  • stat_conf_ellipse: ensure stat returns a data.frame for compatibility with ggplot2 v>=3.4.0
  • stat_compare_means():
    • Unit tests added
    • Updated to use after_stat(p.signif) as the dot-dot notation (..p.signif..) was deprecated in ggplot2 3.4.0 (#509).
  • ggdensity() and gghistogram(): dot-dot notation (..density.., ..count..) replaced by after_stat(density) and after_stat(count), respectively for compatibility with ggplot2 3.4.0.
  • create_aes():
    • Default is now to parse its input, which can be an expression (#348). If you want ggpubr to handle non-standard column names (#229), like A-A, without parsing, then set this option to FALSE using options(ggpubr.parse_aes = FALSE).
    • Supports space in column names like “Dimension 1”
    • Unit tests added
  • Arguments (digits and table.font.size) added to ggsummarystats() for changing the summary table decimal place and text size (#341).
  • In stat_pvalue_manual() the argument hide.ns can be either a logical value (TRUE or FALSE) or a character value (“p” or “p.adj” for filtering out non significant by p-value or adjusted p-values).
  • Now, the x-axis tick label names correctly align with the corresponding ticks when the rotation angle of the texts is set to 90. This is automatically achieved by setting internally vjust = 0.5 (#301).
  • Capital NS. is no longer displayed by stat_compare_means() (#171)
  • Unit tests added forggshistogram() to make sure that it works when:
    • using after_stat(),
    • using after_stat() with trailing space inside parentheses.
  • Unit tests added forggscatter() to make sure that:
    • it works when there is spaces in variable names
    • it can handle non-standard column names when ggpubr.parse_aes global option is set to FALSE (#229)

ggpubr 0.4.0

CRAN release: 2020-06-27

New features

  • New functions added to customize ggtexttable() (#125, #129 and #283):
    • tab_cell_crossout(): cross out a table cell.
    • tab_ncol(), tab_nrow(): returns, respectively, the number of columns and rows in a ggtexttable.
    • tab_add_hline(): Creates horizontal lines or separators at the top or the bottom side of a given specified row.
    • tab_add_vline(): Creates vertical lines or separators at the right or the left side of a given specified column.
    • tab_add_border(), tbody_add_border(), thead_add_border(): Add borders to table; tbody is for table body and thead is for table head.
    • tab_add_title() and tab_add_footnote() to add titles and footnotes (#243).
  • ggpubr functions updated to handle non-standard column names, for example (“A-A”) (#229).
  • New function create_aes() added to create aes mapping from a list. Makes programming easy with ggplot2 (#229).
  • New argument coord.flip added to support adding p-values onto horizontal ggplots (#179). When adding the p-values to a horizontal ggplot (generated using coord_flip()), you need to specify the option coord.flip = TRUE.
  • New errorbar functions - median_hilow_() and median_q1q3() - added (@davidlorenz, #209):
    • median_hilow_(): computes the sample median and a selected pair of outer quantiles having equal tail areas. This function is a reformatted version of Hmisc::smedian.hilow(). The confidence limits are computed as follows: lower.limits = (1-ci)/2 percentiles; upper.limits = (1+ci)/2 percentiles. By default (ci = 0.95), the 2.5th and the 97.5th percentiles are used as the lower and the upper confidence limits, respectively. If you want to use the 25th and the 75th percentiles as the confidence limits, then specify ci = 0.5 or use the function median_q1q3().
    • median_q1q3(): computes the sample median and, the 25th and 75th percentiles. Wrapper around the function median_hilow_() using ci = 0.5.
  • New function get_breaks() added to easily create breaks for numeric axes. Can be used to increase the number of x and y ticks by specifying the option n. It’s also possible to control axis breaks by specifying a step between ticks. For example, if by = 5, a tick mark is shown on every 5 (@Chitanda-Satou, #258).

Major changes

  • The following enhancement has been added to ggscatterhist() (@juliechevalier, #176):
    • the output of ggscatterhist() is now a list of ggplots, containing the main scatter plot (sp) and the marginal plots (xplot and yplot), which can be customized by the end user using the standard ggplot verbs
    • An S3 printing method is now available for an object of class ggscatterhist. The printing method displays the arranged final figure.

Minor changes

  • Now, when creating a box plot with error bars, color and fill arguments are taken into account in the errorbar function (#105).
  • New argument alternative supported in stat_cor() (#276).
  • New argument position in ggline() to make position “dodged” (#52).
  • New argument outlier.shape in ggboxplot(). Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.
  • Sorting can be now disabled in ggdotchart() using the option sorting = "none" (#115, #223).
  • New argument weight added in gghistogram() for creating a weighted histogram (#215)
  • Now ggscaterhist() takes into account the argument position in margin.params when marginal plot is a histogram (#286).
  • ggbarplot() enhanced to better handle the creation of dodged bar plots combined with jitter points (@aherholt, #176)
  • New argument bracket.shorten added in stat_pvalue_manual() and geom_bracket(). a small numeric value in [0-1] for shortening the with of bracket (#285).
  • New argument bracket.nudge.y added in stat_pvalue_manual() and geom_bracket(). Vertical adjustment to nudge brackets by. Useful to move up or move down the bracket. If positive value, brackets will be moved up; if negative value, brackets are moved down (#281).
  • New argument numeric.x.axis added in ggerrorplot(); logical value, If TRUE, x axis will be treated as numeric. Default is FALSE (#280).
  • The option width is now considered in ggadd() for plotting error bars (#278).
  • New argument linetype in ggpaired().
  • geom_exec() used in ggpaired() to add lines between paired points.
  • ggmaplot() now supports two input formats (#198):
    1. baseMean | log2FoldChange|padj: Here, we’ll use log2(baseMean) as the x-axis variable
    2. baseMeanLog2 | log2FoldChange|padj: here, baseMeanLog2 is assumed to be the mean of logged values; so we’ll use it as x-axis variable without any transformation.
  • new arguments added in ggmaplot():
  • In ggadd() the fill argument is considered for jitter points only when the point shape is in 21:25 (@atakanekiz, #148).
  • New argument parse added in ggscatter() and in ggtext(). If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath (#250).
  • New argument stroke supported in ggscatter() and in ggline(). Used only for shapes 21-24 to control the thickness of points border (@bioguy2018, #258).
  • the stat_cor() function code has been simplified. New arguments p.accuracy and r.accuracy added; a real value specifying the number of decimal places of precision for the p-value and the correlation coefficient, respectively. Default is NULL. Use (e.g.) 0.01 to show 2 decimal places of precision (@garthtarr, #186, @raedevan6, #114, #270).

Bug fixes

ggpubr 0.3.0

CRAN release: 2020-05-04

New features

Minor changes

  • New arguments:
    • vjsut in stat_compare_means() to move the text up or down relative to the bracket.
    • type in geom_bracket() to specify label type. Can be “text” or “expression” (for parsing plotmath expression); #253.
    • labeller to the function facet()
    • position in get_legend() to specify legend position
    • legend.grob in ggarrange() to specify a common legend you want to add onto the combined plot.
  • Maintenance adaptation to dplyr new version by removing deprecated functions, such as group_by_, select_, arrange_, etc

Bug fixes

  • Now, Barplots are correctly labelled when custom labels are specified by users (@sekharcu, #234)

ggpubr 0.2.5

CRAN release: 2020-02-13

Minor changes

  • New arguments cor.coef.name in the function stat_cor(). Can be one of “R” (pearson coef), “rho” (spearman coef) and “tau” (kendall coef). Uppercase and lowercase are allowed (@andhamel, #216).
  • New arguments digits, r.digits, p.digits in the function stat_cor(). Integer indicating the number of decimal places (round) or significant digits (signif) to be used for the correlation coefficient and the p-value (@raedevan6, #216).
  • compare_means() adapted to tidyr v>= 1.0.0 by specifying cols in the unnest() function (@Youguang, #216).

ggpubr 0.2.4

CRAN release: 2019-11-14

Minor change

  • unnest adapted to tidyr 1.0.0
  • stat_pvalue_manual() can now handle an rstatix test result containing only one group column.

ggpubr 0.2.3

CRAN release: 2019-09-03

New features

  • New function stat_central_tendency() to add central tendency measures (mean, median, mode) to density and histogram plots
  • New function stat_overlay_normal_density() to overlay normal density plot (with the same mean and SD) to the density distribution of ‘x’.

Minor changes

Bug fixes

ggpubr 0.2.2

CRAN release: 2019-08-07

New features

  • New function geom_bracket() for adding brackets with label annotation to a ggplot. Helpers for adding p-value or significance levels to a plot.

Minor changes

Bug fixes

  • Bug fixes in gghistogram(). Works now when the x variable is R keyword, such as var, mean, etc. (#192)
  • In ggline(), error bars now react automatically to grouping by line type (#191)

ggpubr 0.2.1

CRAN release: 2019-06-23

Minor changes

Bug fixes

ggpubr 0.2

CRAN release: 2018-11-15

Bug fixes

  • P-values for multiple comparisons by group (stat_compare_means()) are now correctly displayed (@elisheva100, #135).

ggpubr 0.1.9

CRAN release: 2018-11-11

Minor changes

  • ggsci palettes have been updated to add new palettes: nejm, jama, ucscgb, d3, locuszoom, igv, startrek, tron, futurama, simpsons (@cbrueffer, #118)

Bug fixes

  • The option ref.group was only considered when the grouping variable contains more than two levels. In that case, each level is compared against the specified reference group. Now, ref.group option is also considered in two samples mean comparisons (@OwenDonohoe, #118)

  • Now, ggqqplot() reacts to the argument conf.int.level (@vsluydts, #123)

  • Added error bar color is now inherited from the main plot (@JesseRop, #109)

ggpubr 0.1.8

CRAN release: 2018-08-30

New features

Minor changes

Bug fixes

ggpubr 0.1.7

CRAN release: 2018-06-23

New features

Minor changes

Bug fixes

  • In ggscatterhist() the x variable was plotted two times, on both the plot x & y margins, instead of having, as expected, a) the x variable on the main plot x margin and 2) the y variable on the main plot y margin. This has been now fixed.
  • In previous version, ggdotchart() sorted automatically within groups when the color argument is specified, even when groups = NULL. This default behaviour has been now removed. Sorting within groups is performed only when the argument group is specified (@sfeds, #90).
  • Now, yticks.by and xticks.by work with NAs (@j3ypi, #89).

ggpubr 0.1.6

CRAN release: 2017-11-14

New features

  • New function ggballoonplot() added to visualize a contingency table.

  • ggdotchart() can be now used to plot multiple groups with position = position_dodge() (@ManuelSpinola, #45).

  • New function ggscatterhist() to create a scatter plot with marginal histograms, density plots and box plots.

  • New theme theme_pubclean(): a clean theme without axis lines, to direct more attention to the data.

  • New arguments in ggarrange() to customize plot labels (@G-Thomson, #41):

    • font.label
    • label.x and label.y
    • hjust and vjust

  • New argument method.args added to stat_compare_means(). A list of additional arguments used for the test method. For example one might use method.args = list(alternative = “greater”) for wilcoxon test (@Nicktz, #41).

  • New argument symnum.args added to stat_compare_means(). A list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns"))

  • New functions table_cell_font() and table_cell_bg() to easily access and change the text font and the background of ggtexttable() cells (@ProbleMaker, #29).

  • New argument numeric.x.axis in ggline(). logical. If TRUE, x axis will be treated as numeric. Default is FALSE. (@mdphan, #35)

  • New argument lab.nb.digits in ggbarplot(). Integer indicating the number of decimal places (round) to be used (#28). Example: lab.nb.digits = 2.

  • New argument tip.length in stat_compare_means(). Numeric vector with the fraction of total height that the bar goes down to indicate the precise column. Default is 0.03. Can be of same length as the number of comparisons to adjust specifically the tip length of each comparison. For example tip.length = c(0.01, 0.03).

Minor changes

  • Now get_legend() returns NULL when the plot doesn’t have legend.

Bug fixes

ggpubr 0.1.5

CRAN release: 2017-08-22

Minor changes

  • In ggpar(), now legend.title can be either a character vector, e.g.: legend.title = “Species” or a list, legend.title = list(color = "Species", linetype = "Species", shape = "Species").

  • New argument ellipse.border.remove in ggscatter() to remove ellipse border lines.

ggscatter(mtcars, x = "mpg", y = "wt",
          color = "cyl",
          ellipse = TRUE, mean.point = TRUE,
          ellipse.border.remove = TRUE)

Bug fixes

ggpubr 0.1.4

CRAN release: 2017-06-28

New features

Minor changes

  • In gghistogram(), density curve and rug react to the fill color.
  • ggarrange():
    • New argument align to specify whether graphs in the grid should be horizontally (“h”) or vertically (“v”) aligned.
    • New argument legend to remove or specify the legend position when arranging multiple plots.
    • New argument common.legend to create a common unique legend for multiple plots.

ggpubr 0.1.3

CRAN release: 2017-06-06

New features

Major changes

  • New arguments in ggpubr functions, see ggboxplot(), ggdotplot(), ggstripchart(), ggviolin(), ggbarplot() and ggline:

    • combine added to combine multiple y variables on the same graph.
    • merge to merge multiple y variables in the same plotting area.
    • select to select which item to display.
    • remove to remove a specific item from a plot.
    • order to order plot items.
    • label, font.label, label.select, repel, label.rectangle to add and customize labels
    • facet.by, panel.labs and short.panel.labs: support for faceting and customization of plot panels

  • New argument grouping.vars in ggtext(). Grouping variables to sort the data by, when the user wants to display the top n up/down labels.

  • New arguments in theme_pubr():

    • border,
    • margin,
    • legend,
    • x.text.angle

Minor changes

  • Now, the argument palette can be also a numeric vector of length(groups); in this case a basic color palette is created using the function grDevices::palette().

Bug fixes

  • Now, ggpar() reacts to palette when length(palette) = 1 and palette is a color name #3.

  • ggmaplot() now handles situations, where there is only upregulated, or downregulated genes.

ggpubr 0.1.2

CRAN release: 2017-03-14

New features

  • New function get_palette() to generate a palette of k colors from ggsci palettes, RColorBrewer palettes and custom color palettes. Useful to extend RColorBrewer and ggsci to support more colors.

Minor changes

  • Now the ggpar() function can handle a list of ggplots.
  • Now the default legend position is right.
  • New argument show.legend.text in the ggscatter() function. Use show.legend.text = FALSE to hide text in the legend.
  • New arguments title, submain, subtitle, caption, font.submain, font.subtitle, font.caption in the ggpar() function.
  • New argument font.family in ggscatter().

Bug fixed

  • Group means for ggdensity (gghistogram) are now shown when data have NA values @chunkaowang, #1

ggpubr 0.1.1

CRAN release: 2016-12-05

New features

  • New function ggtext() for textual annotation.
  • New argument star.plot in ggscatter(). A logical value. If TRUE, a star plot is generated.
  • New helper function geom_exec(). A helper function used by ggpubr functions to execute any geom_xx functions in ggplot2. Useful only when you want to call a geom_xx function without worrying about the arguments to put in ggplot2::aes().
  • New arguments sort.val and top in ggbarplot().
    • sort.val: a string specifying whether the value should be sorted. Allowed values are “none” (no sorting), “asc” (for ascending) or “desc” (for descending).
    • top: a numeric value specifying the number of top elements to be shown.
  • New function theme_classic2() added. Classic theme with axis lines.

Minor changes

# Example
ggboxplot(iris$Sepal.Length)
  • Now, in gghistogram(), when add_density = TRUE, y scale remains = “..count..”.
  • Now, default theme changed to theme_classic2()
  • Default point size and line size set to NULL

ggpubr 0.1.0

CRAN release: 2016-07-20

Plot one variable - X: Continuous

  • ggdensity(): Density plot
  • gghistogram(): Histogram plot
  • ggecdf(): Empirical cumulative density function
  • ggqqplot(): QQ plots

Plot two variables - X & Y: Discrete X and Continuous Y

  • ggboxplot(): Box plot
  • ggviolin(): Violin plot
  • ggdotplot(): Dot plot
  • ggstripchart(): Stripchart (jitter)
  • ggbarplot(): Bar plot
  • ggline(): Line plot
  • ggerrorplot(): Error plot
  • ggpie(): Pie chart
  • ggdotchart(): Cleveland’s dot plots

Plot two continuous variables

  • ggscatter(): Scatter plot

Graphical parameters

  • ggpar(): Change graphical parameters
  • show_line_type(): Line types available in R
  • show_point_shapes(): Point shapes available in R
  • theme_pubr(): Create a publication ready theme
  • labs_pubr(): Format only plot labels to a publication ready style

Genomics

  • ggmaplot(): MA-plot from means and log fold changes

Data

  • diff_express: Differential gene expression analysis results

Other

  • desc_statby(): Descriptive statistics by groups
  • stat_chull(): Plot convex hull of a set of points
  • stat_conf_ellipse(): Plot confidence ellipses
  • stat_mean(): Draw group mean points