% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/boxviolinplot.R
\name{BoxViolinPlot}
\alias{BoxViolinPlot}
\title{Box / Violin / Bar / Beeswarm plot (internal)}
\usage{
BoxViolinPlot(
  data,
  x,
  x_sep = "_",
  y = NULL,
  base = c("box", "violin", "bar", "none"),
  in_form = c("long", "wide"),
  split_by = NULL,
  split_by_sep = "_",
  symnum_args = NULL,
  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,
  fill_mode = ifelse(!is.null(group_by), "dodge", "x"),
  palreverse = FALSE,
  position_dodge_preserve = "total",
  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,
  jitter_width = NULL,
  jitter_height = 0,
  stack = FALSE,
  y_max = NULL,
  y_min = NULL,
  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,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)
}
\arguments{
\item{data}{A data frame.}

\item{x}{A character string specifying the column name of the data frame to plot for the x-axis.}

\item{x_sep}{A character string to join multiple \code{x} columns.
Default \code{"_"}.}

\item{y}{A character string specifying the column name of the data frame to plot for the y-axis.}

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

\item{in_form}{A character string: \code{"long"} (default) or
\code{"wide"}.  In wide form, \code{x} columns are pivoted to long
format.}

\item{split_by}{The column(s) to split the data by for separate sub-plots.}

\item{split_by_sep}{Separator for concatenated \code{split_by} columns.}

\item{symnum_args}{A list of arguments passed to
\code{\link[stats]{symnum}} for symbolic p-value coding.}

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

\item{flip}{Logical; if \code{TRUE}, swap the x and y axes.}

\item{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 \code{x}, \code{group_by}, \code{fill_by}, etc.
\itemize{
\item{\code{FALSE} (default): Drop empty factor levels from the data before plotting.}
\item{\code{TRUE}: Keep empty factor levels and show them as a separate category in the plot.}
\item{\code{"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: \code{levels}}
}}

\item{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 \code{x}, \code{group_by}, \code{fill_by}, etc.}

\item{group_by}{Columns to group the data for plotting
For those plotting functions that do not support multiple groups,
They will be concatenated into one column, using \code{group_by_sep} as the separator}

\item{group_by_sep}{The separator for multiple group_by columns. See \code{group_by}}

\item{group_name}{A character string for the dodge legend title.}

\item{paired_by}{A character string naming a column that identifies
paired observations.  Forces \code{add_point = TRUE} and connects
paired observations with lines.}

\item{x_text_angle}{A numeric value specifying the angle of the x-axis text.}

\item{step_increase}{Fractional step increase for stacking significance
brackets when multiple comparisons exist.}

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

\item{palreverse}{A logical value indicating whether to reverse the palette. Default is FALSE.}

\item{position_dodge_preserve}{Passed to
\code{\link[ggplot2]{position_dodge}()}: \code{"total"} preserves the
overall group width; \code{"single"} preserves individual element width.}

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

\item{theme_args}{A list of arguments to pass to the theme function.}

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

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

\item{alpha}{A numeric value specifying the transparency of the plot.}

\item{aspect.ratio}{A numeric value specifying the aspect ratio of the plot.}

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

\item{legend.direction}{A character string specifying the direction of the legend.}

\item{add_point}{Logical; add jittered or beeswarm points to the plot.}

\item{pt_color}{Colour of the points.  When \code{add_beeswarm = TRUE}
and \code{pt_color} is \code{NULL}, points are coloured by the fill
variable.}

\item{pt_size}{Numeric size of the points.  Default computed from
data size: \code{min(3000 / nrow(data), 0.6)}.}

\item{pt_alpha}{Numeric transparency of the points.}

\item{jitter_width}{Numeric width of the jitter.  Defaults to
\code{0.5}, but set to \code{0} when \code{paired_by} is provided.}

\item{jitter_height}{Numeric height of the jitter.  Default \code{0}.}

\item{stack}{Logical; stack facetted panels in a compact layout with
shared strip labels.}

\item{y_max, y_min}{Numeric y-axis limits, or quantile notation strings
(e.g., \code{"q95"} for the 95th percentile, \code{"q5"} for the
5th percentile).}

\item{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.}

\item{add_beeswarm}{Logical; use \code{ggbeeswarm::geom_beeswarm()} for
non-overlapping point layout instead of jitter.  Requires the
\code{ggbeeswarm} package.}

\item{beeswarm_method}{Beeswarm layout method: \code{"swarm"},
\code{"compactswarm"}, \code{"hex"}, \code{"square"}, or
\code{"center"}.}

\item{beeswarm_cex}{Numeric scaling for point spacing.  Larger values
spread points more.}

\item{beeswarm_priority}{Point layout priority: \code{"ascending"},
\code{"descending"}, \code{"density"}, or \code{"random"}.}

\item{beeswarm_dodge}{Numeric dodge width for beeswarm points when
\code{group_by} is provided.  Default \code{0.9}.}

\item{add_box}{Logical; overlay a box plot on the primary geometry.
Mutually exclusive with \code{base = "box"} and \code{base = "bar"}.}

\item{box_color}{Colour of the overlaid box plot outline and fill.}

\item{box_width}{Width of the overlaid box plot.}

\item{box_ptsize}{Size of the median point in the overlaid box plot.}

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

\item{errorbar_color}{Colour of the error bar lines and caps.}

\item{errorbar_width}{Width of the error bar caps.}

\item{errorbar_linewidth}{Line width of the error bars.}

\item{add_trend}{Logical; add trend lines connecting group medians.}

\item{trend_color}{Colour of the trend line.  When \code{NULL} and
\code{group_by} is present, lines are coloured per group.}

\item{trend_linewidth}{Width of the trend line.}

\item{trend_ptsize}{Size of the trend line points.}

\item{add_stat}{A summary function (e.g., \code{mean}, \code{median}) to
display as a point with a shape legend entry.}

\item{stat_name}{Legend title for the stat summary shape.}

\item{stat_color}{Colour of the stat summary point.}

\item{stat_size}{Size of the stat summary point.}

\item{stat_stroke}{Stroke width of the stat summary point.}

\item{stat_shape}{Shape (an integer) for the stat summary point.  Uses
\code{scale_shape_identity()} so the shape is rendered directly.}

\item{add_bg}{Logical; add alternating background stripes.}

\item{bg_palette}{Palette for the background stripes.}

\item{bg_palcolor}{Custom colours for the background stripes.}

\item{bg_alpha}{Alpha transparency for the background stripes.}

\item{add_line}{A numeric y-intercept for a horizontal reference line.}

\item{line_color}{Colour of the reference line.}

\item{line_width}{Width of the reference line.}

\item{line_type}{Linetype of the reference line.}

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

\item{highlight_color}{Colour of highlighted points.}

\item{highlight_size}{Size of highlighted points.}

\item{highlight_alpha}{Alpha of highlighted points.}

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

\item{ref_group}{A character string specifying the reference group for
comparisons.}

\item{pairwise_method}{Method for pairwise tests.  Default
\code{"wilcox.test"}.}

\item{multiplegroup_comparisons}{Logical; perform an omnibus test
(e.g., Kruskal-Wallis) across all groups.}

\item{multiple_method}{Method for the omnibus test.  Default
\code{"kruskal.test"}.}

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

\item{sig_labelsize}{Size of the significance label text.}

\item{hide_ns}{Logical; hide non-significant comparison labels.}

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

\item{facet_scales}{Whether to scale the axes of facets. Default is "fixed"
Other options are "free", "free_x", "free_y". See \code{ggplot2::facet_wrap}}

\item{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.}

\item{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.}

\item{facet_byrow}{A logical value indicating whether to fill the plots by row. Default is TRUE.}

\item{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.}

\item{subtitle}{A character string specifying the subtitle of the plot.}

\item{xlab}{A character string specifying the x-axis label.}

\item{ylab}{A character string specifying the y-axis label.}

\item{seed}{A numeric seed for reproducibility.}

\item{combine}{Logical; when \code{TRUE} (default), returns a combined
\code{patchwork} object.  When \code{FALSE}, returns a named list of
\code{ggplot} objects.}

\item{ncol, nrow}{Integer number of columns / rows for the combined layout.}

\item{byrow}{Logical; fill the combined layout by row (default \code{TRUE}).}

\item{axes, axis_titles}{Character strings for axis handling in the
combined layout.}

\item{guides}{Character string for legend collection across panels.}

\item{design}{A custom layout design for the combined plot.}

\item{...}{Additional arguments.}
}
\value{
A \code{ggplot} object, a \code{patchwork} object, or a named list
of \code{ggplot} objects (when \code{combine = FALSE}), each with
\code{height} and \code{width} attributes in inches.
}
\description{
Internal wrapper that handles \code{split_by} processing and dispatches
to \code{\link{BoxViolinPlotAtomic}} for each split.  This is the
intermediate layer between the three public APIs
(\code{\link{BoxPlot}}, \code{\link{ViolinPlot}}, and
\code{\link{BeeswarmPlot}}) and the core implementation.
}
\section{split_by workflow}{

When \code{split_by} is provided:
\enumerate{
\item \code{\link{check_keep_na}()} and \code{\link{check_keep_empty}()}
normalise the \code{keep_na} / \code{keep_empty} arguments.
\item The \code{split_by} column is validated and its NA / empty levels
are processed.  It is then removed from the per-column lists.
\item The data is split by \code{split_by} (preserving level order).
If \code{split_by} is \code{NULL}, the data is wrapped in a
single-element list with name \code{"..."}.
\item Per-split \code{palette}, \code{palcolor},
\code{legend.position}, and \code{legend.direction} are resolved.
\item \code{\link{BoxViolinPlotAtomic}()} is called for each split.
When \code{title} is a function, it receives the split level name
for dynamic titles.
\item Results are combined via \code{\link{combine_plots}()}.
}
}

\keyword{internal}
