% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/densityplot.R
\name{RidgePlot}
\alias{RidgePlot}
\title{Ridge Plot}
\usage{
RidgePlot(
  data,
  x = NULL,
  in_form = c("long", "wide"),
  split_by = NULL,
  split_by_sep = "_",
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  scale = NULL,
  keep_na = FALSE,
  keep_empty = FALSE,
  add_vline = NULL,
  vline_type = "solid",
  vline_color = TRUE,
  vline_width = 0.5,
  vline_alpha = 1,
  flip = FALSE,
  alpha = 0.8,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  x_text_angle = 90,
  x_min = NULL,
  x_max = NULL,
  reverse = FALSE,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = "none",
  legend.direction = "vertical",
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 8525,
  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{in_form}{A character string specifying whether \code{data} is in
\code{"long"} (default) or \code{"wide"} format.}

\item{split_by}{The column(s) to split data by and plot separately.
When \code{combine = TRUE}, the combined plot's data (\code{p$data})
contains the rows of every split, tagged with the \code{split_by}
column. For ggraph-based plots (e.g. \code{\link{Network}},
\code{\link{ClustreePlot}}), the node layout of every split is
exposed with the split column, and the original link rows (also
tagged with the \code{split_by} column) are available as the
\code{"edges"} attribute of the data.}

\item{split_by_sep}{The separator for multiple split_by columns. See \code{split_by}}

\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 used as the legend title for the
\code{group_by} fill aesthetic. Defaults to the (concatenated) \code{group_by}
column name.}

\item{scale}{A numeric value controlling the vertical overlap of ridges.
Passed to \code{ggridges::geom_density_ridges(scale = ...)}. Smaller values
increase overlap. When \code{NULL}, ggridges auto-computes the scale.}

\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{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{add_vline}{A specification for vertical reference lines:
\itemize{
\item \code{NULL} or \code{FALSE}: no lines.
\item \code{TRUE}: draw a line at the mean of each group.
\item A numeric vector: draw the same lines for all groups.
\item A named list of numeric vectors: per-group lines, where names should
match \code{group_by} levels.
}}

\item{vline_type}{A character string specifying the line type for the
vertical reference lines. Passed as \code{linetype} to \code{geom_vline()}.
Default: \code{"solid"}.}

\item{vline_color}{The colour of the vertical reference lines:
\itemize{
\item A literal colour value or vector (recycled): applied directly.
\item \code{TRUE} (default): each line is coloured with a darkened blend of
the corresponding ridge fill colour, computed via
\code{blend_colors(mode = "multiply")}.
}}

\item{vline_width}{A numeric value for the thickness of the vertical
reference lines. Passed as \code{linewidth} to \code{geom_vline()}.
Default: \code{0.5}.}

\item{vline_alpha}{A numeric value in \verb{[0, 1]} for the transparency of
the vertical reference lines. Default: \code{1}.}

\item{flip}{A logical value. If \code{TRUE}, the axes are swapped via
\code{coord_flip()}. X-axis text angle and grid-line placement are adjusted
accordingly.}

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

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

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

\item{x_min, x_max}{Numeric limits for the x-axis. When \code{NULL} (default),
limits are determined from the data range. Passed to \code{scale_x_continuous(limits = ...)}.}

\item{reverse}{A logical value. If \code{TRUE}, the y-axis group order is
reversed. NA groups are renamed to the literal string \code{"NA"} and
placed at the end.}

\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{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{combine}{Whether to combine the plots into one when facet is FALSE. Default is TRUE.}

\item{nrow}{A numeric value specifying the number of rows in the facet.}

\item{ncol}{A numeric value specifying the number of columns in the facet.}

\item{byrow}{A logical value indicating whether to fill the plots by row.}

\item{seed}{The random seed to use. Default is 8525.}

\item{axes}{A string specifying how axes should be treated. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'keep' will retain all axes in individual plots.
\item 'collect' will remove duplicated axes when placed in the same run of rows or columns of the layout.
\item 'collect_x' and 'collect_y' will remove duplicated x-axes in the columns or duplicated y-axes in the rows respectively.
}}

\item{axis_titles}{A string specifying how axis titltes should be treated. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'keep' will retain all axis titles in individual plots.
\item 'collect' will remove duplicated titles in one direction and merge titles in the opposite direction.
\item 'collect_x' and 'collect_y' control this for x-axis titles and y-axis titles respectively.
}}

\item{guides}{A string specifying how guides should be treated in the layout. Passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE.
Options are:
\itemize{
\item 'collect' will collect guides below to the given nesting level, removing duplicates.
\item 'keep' will stop collection at this level and let guides be placed alongside their plot.
\item 'auto' will allow guides to be collected if a upper level tries, but place them alongside the plot if not.
}}

\item{design}{Specification of the location of areas in the layout, passed to \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}.
Only relevant when \code{split_by} is used and \code{combine} is TRUE. When specified, \code{nrow}, \code{ncol}, and \code{byrow} are ignored.
See \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}} for more details.}

\item{...}{Additional arguments.}
}
\value{
A \code{ggplot} object (single plot), a \code{patchwork} / \code{wrap_plots} object
(when \code{split_by} is provided and \code{combine = TRUE}), or a list of \code{ggplot}
objects (when \code{split_by} is provided and \code{combine = FALSE}).
}
\description{
Ridge (joy) plot for visualising the distribution of a numeric variable across
multiple groups. Each group is rendered as a partially overlapping density
curve along the y-axis, making it easy to compare distribution shapes, central
tendency, and spread across categories.

The function supports both \strong{long} and \strong{wide} data formats:
\itemize{
\item \strong{Long form} (\code{in_form = "long"}, default) — a numeric column (\code{x}) plus a
factor column (\code{group_by}) whose levels become the y-axis ridges.
\item \strong{Wide form} (\code{in_form = "wide"}) — multiple numeric columns listed in
\code{group_by} are gathered internally into long form.
}

Optional vertical reference lines (\code{add_vline}) can mark group means,
specific values, or per-group thresholds. Supports faceting, split-by
splitting, and full palette customisation.
}
\section{split_by Workflow}{


When \code{split_by} is specified, \code{RidgePlot()} executes the following pipeline:
\enumerate{
\item \strong{Argument validation} — \code{validate_common_args()} checks the seed and
facet-by consistency.
\item \strong{NA / empty normalisation} — \code{check_keep_na()} / \code{check_keep_empty()}
convert \code{keep_na} / \code{keep_empty} to per-column lists.
\item \strong{Theme resolution} — \code{process_theme()} resolves the theme string to a
theme function.
\item \strong{Split column resolution} — \code{check_columns()} validates \code{split_by}
(force_factor, concat_multi).
\item \strong{Pre-filtering} — \code{process_keep_na_empty()} removes NA / empty levels
from the split column, then \code{data} is split by \code{split_by} levels (order
preserved).
\item \strong{Per-split parameter resolution} — \code{check_palette()},
\code{check_palcolor()}, \code{check_legend()} resolve palette, palcolor,
legend.position, and legend.direction for each split.
\item \strong{Per-split dispatch} — each split is passed to \code{RidgePlotAtomic()} with
its resolved parameters. Title defaults to the split level name unless
\code{title} is a function (in which case it is called with the default).
\item \strong{Combination} — \code{combine_plots()} assembles the list of plots via
\code{patchwork::wrap_plots()}, applying \code{nrow}, \code{ncol}, \code{byrow}, \code{axes},
\code{axis_titles}, \code{guides}, and \code{design}.
}
}

\examples{
\donttest{
set.seed(8525)
data <- data.frame(
   x = c(rnorm(250, -1), rnorm(250, 1)),
   group = factor(rep(c("A", NA, LETTERS[3:5]), each = 100), levels = LETTERS[1:6])
)

# basic usage
RidgePlot(data, x = "x")  # single ridge (no group_by)
RidgePlot(data, x = "x", add_vline = 0, vline_color = "black")

# grouped ridges
RidgePlot(data, x = "x", group_by = "group")
RidgePlot(data, x = "x", group_by = "group",
   keep_na = TRUE, keep_empty = TRUE)
RidgePlot(data, x = "x", group_by = "group", reverse = TRUE)
RidgePlot(data, x = "x", group_by = "group",
   add_vline = TRUE, vline_color = TRUE, alpha = 0.7)

# faceting
RidgePlot(data, x = "x", facet_by = "group",
   keep_na = TRUE, keep_empty = TRUE)

# wide form
data_wide <- data.frame(
   A = rnorm(100),
   B = rnorm(100),
   C = rnorm(100),
   D = rnorm(100),
   E = rnorm(100),
   group = sample(letters[1:4], 100, replace = TRUE)
)
RidgePlot(data_wide, group_by = LETTERS[1:5], in_form = "wide")
RidgePlot(data_wide, group_by = LETTERS[1:5], in_form = "wide", facet_by = "group")

# split_by with per-split palettes
RidgePlot(data_wide, group_by = LETTERS[1:5], in_form = "wide", split_by = "group",
   palette = list(a = "Reds", b = "Blues", c = "Greens", d = "Purples"))
}
}
