ggpubr 1.0.0

ggpubr 1.0.0 is on CRAN: https://cran.r-project.org/package=ggpubr

Install with:

install.packages("ggpubr")

---

New features

New functions

• Added format_p_value(), get_p_format_style(), and list_p_format_styles().
• Added style presets (default, apa, nejm, lancet, ama, graphpad, scientific).

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

• Contributor: Laszlo Erdey (Faculty of Economics and Business, University of Debrecen, Hungary).
• Thanks to @gumeo (#418), @byzheng (#608) and @JulesROBIN15 (#625) whose pull
  requests proposed features shipped in this release: the stat_cor()
  confidence interval, the stat_cor() RMSE label, and a manual number of
  comparisons for p-value adjustment in geom_pwc()/stat_pwc().

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).