Atomic Box / Violin / Bar / Beeswarm plot (internal) — BoxViolinPlotAtomic • plotthis

Core implementation for drawing box plots, violin plots, bar plots (mean ± error bars), or beeswarm plots. This is the workhorse behind BoxPlot, ViolinPlot, and BeeswarmPlot — it takes a single data frame (no split_by support) and returns a ggplot object.

The base parameter selects the primary geometry:

"box" — geom_boxplot()
"violin" — geom_violin()
"bar" — stat_summary(fun = mean, geom = "col") with optional error bars (SEM, SD, or CI).
"none" — no primary geometry (used by BeeswarmPlot to draw beeswarm points alone).

Usage

BoxViolinPlotAtomic(
  data,
  x,
  x_sep = "_",
  y = NULL,
  base = c("box", "violin", "bar", "none"),
  in_form = c("long", "wide"),
  sort_x = NULL,
  flip = FALSE,
  keep_empty = FALSE,
  keep_na = FALSE,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  paired_by = NULL,
  x_text_angle = ifelse(isTRUE(flip), 0, 45),
  step_increase = 0.1,
  position_dodge_preserve = "total",
  fill_mode = ifelse(!is.null(group_by), "dodge", "x"),
  palreverse = FALSE,
  symnum_args = NULL,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  add_point = FALSE,
  pt_color = if (isTRUE(add_beeswarm)) NULL else "grey30",
  pt_size = NULL,
  pt_alpha = 1,
  y_nbreaks = 4,
  jitter_width = NULL,
  jitter_height = 0,
  stack = FALSE,
  y_max = NULL,
  y_min = NULL,
  y_trans = "identity",
  y_brackets = NULL,
  add_beeswarm = FALSE,
  beeswarm_method = "swarm",
  beeswarm_cex = 1,
  beeswarm_priority = "ascending",
  beeswarm_dodge = 0.9,
  add_box = FALSE,
  box_color = "black",
  box_width = 0.1,
  box_ptsize = 2.5,
  add_errorbar = "SEM",
  errorbar_color = "grey20",
  errorbar_width = 0.4,
  errorbar_linewidth = 0.6,
  add_trend = FALSE,
  trend_color = NULL,
  trend_linewidth = 1,
  trend_ptsize = 2,
  add_stat = NULL,
  stat_name = NULL,
  stat_color = "black",
  stat_size = 1,
  stat_stroke = 1,
  stat_shape = 25,
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_line = NULL,
  line_color = "red2",
  line_width = 0.6,
  line_type = 2,
  highlight = NULL,
  highlight_color = "red2",
  highlight_size = 1,
  highlight_alpha = 1,
  comparisons = NULL,
  ref_group = NULL,
  pairwise_method = "wilcox.test",
  multiplegroup_comparisons = FALSE,
  multiple_method = "kruskal.test",
  sig_label = "p.format",
  sig_labelsize = 3.5,
  hide_ns = FALSE,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  ...
)

Arguments

data

A data frame.

x

A character string of column name(s) for the x-axis. Character/factor columns are expected. Multiple columns are concatenated with x_sep.

x_sep

A character string to join multiple x columns. Default "_".

y

A character string of the numeric column for the y-axis. Not required when in_form = "wide" (data values are taken from the x columns).

base

A character string specifying the primary plot type: "box" (box plot), "violin" (violin plot), "bar" (mean bars with optional error bars), or "none" (no primary geometry, used by beeswarm plots).

in_form

A character string: "long" (default) or "wide". In wide form, x columns are pivoted to long format.

sort_x

An R expression string (e.g., "mean(y)") to order x-axis categories. Default NULL keeps the original order. When keep_empty_x is TRUE, empty levels are placed last.

flip

Logical; if TRUE, swap the x and y axes.

keep_empty

One of FALSE, TRUE and "level". It can also take a named list to specify different behavior for different columns. Without a named list, the behavior applies to the categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

FALSE (default): Drop empty factor levels from the data before plotting.
TRUE: Keep empty factor levels and show them as a separate category in the plot.
"level": Keep empty factor levels, but do not show them in the plot. But they will be assigned colors from the palette to maintain consistency across multiple plots. Alias: levels

keep_na

A logical value or a character to replace the NA values in the data. It can also take a named list to specify different behavior for different columns. If TRUE or NA, NA values will be replaced with NA. If FALSE, NA values will be removed from the data before plotting. If a character string is provided, NA values will be replaced with the provided string. If a named vector/list is provided, the names should be the column names to apply the behavior to, and the values should be one of TRUE, FALSE, or a character string. Without a named vector/list, the behavior applies to categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

group_by

A character vector of column name(s) to dodge the boxes/violins by. Multiple columns are concatenated with group_by_sep.

group_by_sep

A character string to separate concatenated group_by columns. Default "_".

group_name

A character string for the dodge legend title.

paired_by

A character string naming a column that identifies paired observations. Forces add_point = TRUE and connects paired observations with lines.

x_text_angle

A numeric value specifying the angle of the x-axis text.

step_increase

Fractional step increase for stacking significance brackets when multiple comparisons exist.

position_dodge_preserve

Passed to position_dodge(): "total" preserves the overall group width; "single" preserves individual element width.

fill_mode

A character string controlling fill colour mapping: "dodge" (fill by group_by, discrete), "x" (fill by x-axis categories, discrete), "mean" or "median" (fill by pre-computed statistic, continuous gradient).

palreverse

A logical value indicating whether to reverse the palette. Default is FALSE.

symnum_args

A list of arguments passed to symnum for symbolic p-value coding.

theme

A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".

theme_args

A list of arguments to pass to the theme function.

palette

A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.

palcolor

A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).

alpha

A numeric value specifying the transparency of the plot.

aspect.ratio

A numeric value specifying the aspect ratio of the plot.

legend.position

A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".

legend.direction

A character string specifying the direction of the legend.

add_point

Logical; add jittered or beeswarm points to the plot.

pt_color

Colour of the points. When add_beeswarm = TRUE and pt_color is NULL, points are coloured by the fill variable.

pt_size

Numeric size of the points. Default computed from data size: min(3000 / nrow(data), 0.6).

pt_alpha

Numeric transparency of the points.

y_nbreaks

Integer number of y-axis breaks.

jitter_width

Numeric width of the jitter. Defaults to 0.5, but set to 0 when paired_by is provided.

jitter_height

Numeric height of the jitter. Default 0.

stack

Logical; stack facetted panels in a compact layout with shared strip labels.

y_max, y_min

Numeric y-axis limits, or quantile notation strings (e.g., "q95" for the 95th percentile, "q5" for the 5th percentile).

y_trans

A character string for y-axis transformation (e.g., "log10").

y_brackets

Numeric y-axis position for significance brackets (or p-value labels for multiple comparisons). If NULL, the brackets are placed above the maximum y-value.

add_beeswarm

Logical; use ggbeeswarm::geom_beeswarm() for non-overlapping point layout instead of jitter. Requires the ggbeeswarm package.

beeswarm_method

Beeswarm layout method: "swarm", "compactswarm", "hex", "square", or "center".

beeswarm_cex

Numeric scaling for point spacing. Larger values spread points more.

beeswarm_priority

Point layout priority: "ascending", "descending", "density", or "random".

beeswarm_dodge

Numeric dodge width for beeswarm points when group_by is provided. Default 0.9.

add_box

Logical; overlay a box plot on the primary geometry. Mutually exclusive with base = "box" and base = "bar".

box_color

Colour of the overlaid box plot outline and fill.

box_width

Width of the overlaid box plot.

box_ptsize

Size of the median point in the overlaid box plot.

add_errorbar

Type of error bars for bar plots (base = "bar"): "SEM" (standard error of the mean, default), "SD" (standard deviation), "CI" or "CI95" (95\ interval), or "none". Silently ignored for non-bar bases.

errorbar_color

Colour of the error bar lines and caps.

errorbar_width

Width of the error bar caps.

errorbar_linewidth

Line width of the error bars.

add_trend

Logical; add trend lines connecting group medians.

trend_color

Colour of the trend line. When NULL and group_by is present, lines are coloured per group.

trend_linewidth

Width of the trend line.

trend_ptsize

Size of the trend line points.

add_stat

A summary function (e.g., mean, median) to display as a point with a shape legend entry.

stat_name

Legend title for the stat summary shape.

stat_color

Colour of the stat summary point.

stat_size

Size of the stat summary point.

stat_stroke

Stroke width of the stat summary point.

stat_shape

Shape (an integer) for the stat summary point. Uses scale_shape_identity() so the shape is rendered directly.

add_bg

Logical; add alternating background stripes.

bg_palette

Palette for the background stripes.

bg_palcolor

Custom colours for the background stripes.

bg_alpha

Alpha transparency for the background stripes.

add_line

A numeric y-intercept for a horizontal reference line.

line_color

Colour of the reference line.

line_width

Width of the reference line.

line_type

Linetype of the reference line.

highlight

A specification of points to highlight: TRUE (all), a numeric index vector, a logical expression string, or a character vector of row names.

highlight_color

Colour of highlighted points.

highlight_size

Size of highlighted points.

highlight_alpha

Alpha of highlighted points.

comparisons

A logical value (TRUE for all pairs) or a list of two-element vectors specifying pairwise comparisons. Only available when fill_mode = "dodge" (i.e., group_by is present).

ref_group

A character string specifying the reference group for comparisons.

pairwise_method

Method for pairwise tests. Default "wilcox.test".

multiplegroup_comparisons

Logical; perform an omnibus test (e.g., Kruskal-Wallis) across all groups.

multiple_method

Method for the omnibus test. Default "kruskal.test".

sig_label

Label format for significance annotations. For pairwise comparisons: "p.format", "p.signif", or a glue template (e.g., "p = {p}"). For multiple-group tests: "p.format" or "p.signif".

sig_labelsize

Size of the significance label text.

hide_ns

Logical; hide non-significant comparison labels.

facet_by

A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by split_by and generate multiple plots and combine them into one using patchwork::wrap_plots

facet_scales

Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See ggplot2::facet_wrap

facet_ncol

A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.

facet_nrow

A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.

facet_byrow

A logical value indicating whether to fill the plots by row. Default is TRUE.

title

A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.

subtitle

A character string specifying the subtitle of the plot.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

seed

The random seed to use. Default is 8525.

...

Additional arguments.

Value

A ggplot object, possibly faceted, with height and width attributes (in inches) attached.

Architecture

Wide-to-long conversion — when in_form = "wide", data is pivoted via tidyr::pivot_longer(). The keep_na / keep_empty lists are filtered to the new column names.
Column resolution — x, y, group_by, facet_by, and paired_by are validated via check_columns.
NA / empty-level handling — per-column keep_empty settings are extracted for x, group_by, and facet_by independently.
Beeswarm validation — if add_beeswarm = TRUE, the ggbeeswarm package is required. Beeswarm is disabled (with a warning) when paired_by is provided.
Paired data validation — structural checks ensure each (x, paired_by) combination has exactly 2 observations (one per group when group_by is present). Paired observations force add_point = TRUE.
Summary statistics — .y_mean and .y_median are pre-computed per (x, group_by, facet_by) for use in trend lines and fill modes.
y-axis limits — y_max / y_min accept numeric values or quantile notation ("q95", "q5"). For bar plots, the limit is extended upward by the error bar extent.
Highlight — highlight can be TRUE (all points), a numeric index vector, a logical expression string, or a character vector of row names.
sort_x — an R expression string (e.g., "mean(y)") evaluated per x-level to reorder categories.
Flip transformation — when flip = TRUE, factor levels are reversed and aspect.ratio is inverted.
Base geometry — the primary geom is added: geom_boxplot(), geom_violin(), or stat_summary(fun = mean, geom = "col"). Error bars (SEM / SD / CI) are layered on bar plots via a custom stat_summary(fun.data = ...).
Fill mode — fill_mode controls colour mapping:
- "dodge" — fill by group_by (discrete).
- "x" — fill by x-axis categories (discrete).
- "mean" / "median" — fill by pre-computed mean/median (continuous gradient).
Box overlay — when add_box = TRUE on a non-box base, a box plot is overlaid via ggnewscale::new_scale_fill() with a white fill/black outline.
Statistical comparisons — two pathways:
- Pairwise (comparisons) — uses ggpubr::geom_pwc() with automatic or explicit comparison pairs. Data is preprocessed to avoid test failures from zero-variance or all-NA groups.
- Multiple-group (multiplegroup_comparisons) — uses ggpubr::stat_compare_means() for omnibus tests (e.g., Kruskal-Wallis).
After comparison layers are added, y_max_use is expanded to accommodate significance brackets.
Points — jittered points (geom_point() with position_jitterdodge) or beeswarm points (ggbeeswarm::geom_beeswarm()). Paired observations add connecting lines (geom_line()) between matched subjects.
Trend lines — stat_summary(fun = first) draws lines connecting group medians. When trend_color is NULL and group_by is present, lines are coloured per group.
Reference lines — geom_hline() at the specified y-intercept.
Stat summary points — a custom stat_summary() point layer displaying a user-specified summary statistic (e.g., mean) with a shape legend entry.
Stack layout — when stack = TRUE, facets are arranged with shared strip labels and negative panel spacing for a compact stacked appearance.
Dimension calculation — calculate_plot_dimensions() accounts for the number of x-levels × dodge groups, flip state, and stack layout adjustments. Minimum dimensions are enforced from label character widths.
Faceting — facet_plot() wraps the result with the appropriate strip position based on flip/stack state.