% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jitterplot.R
\name{JitterPlot}
\alias{JitterPlot}
\title{Jitter plot}
\usage{
JitterPlot(
  data,
  x,
  x_sep = "_",
  y = NULL,
  in_form = c("long", "wide"),
  split_by = NULL,
  split_by_sep = "_",
  keep_na = FALSE,
  keep_empty = FALSE,
  sort_x = c("none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc",
    "median"),
  flip = FALSE,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  x_text_angle = 0,
  order_by = "-({y}^2 + {size_by}^2)",
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  shape = 21,
  border = "black",
  size_by = 2,
  size_name = NULL,
  size_trans = NULL,
  y_nbreaks = 4,
  jitter_width = 0.5,
  jitter_height = 0,
  y_max = NULL,
  y_min = NULL,
  y_trans = "identity",
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_hline = NULL,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  labels = NULL,
  label_by = NULL,
  nlabel = 5,
  label_size = 3,
  label_fg = "black",
  label_bg = "white",
  label_bg_r = 0.1,
  highlight = NULL,
  highlight_color = "red2",
  highlight_size = 1,
  highlight_alpha = 1,
  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 for the x-axis.
Must be character or factor.  Multiple columns can be provided; they are
concatenated with \code{x_sep} as the separator.  When \code{in_form} is
\code{"wide"}, the \code{x} columns are used as key columns and pivoted
to long format (they are not concatenated).}

\item{x_sep}{A character string used to join multiple \code{x} columns.
Default \code{"_"}.  Ignored when \code{x} is a single column or when
\code{in_form} is \code{"wide"}.}

\item{y}{A character string specifying the numeric column for the y-axis.
Required when \code{in_form} is \code{"long"} (default).  When
\code{in_form} is \code{"wide"}, \code{y} is not required — the values
under the \code{x} columns are used as y-values.}

\item{in_form}{A character string specifying the input data format.  Either
\code{"long"} (default) or \code{"wide"}.  In \code{"long"} format,
\code{x} and \code{y} are separate columns.  In \code{"wide"} format, the
\code{x} columns contain the y-values and are pivoted to a key-value pair.}

\item{split_by}{The column(s) to split the data by and produce separate
sub-plots.  Multiple columns are concatenated with \code{split_by_sep}.}

\item{split_by_sep}{A character string to separate concatenated
\code{split_by} columns.  Default \code{"_"}.}

\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{sort_x}{A character string controlling x-axis level reordering by
y-value summaries.  One of \code{"none"}, \code{"mean_asc"},
\code{"mean_desc"}, \code{"mean"}, \code{"median_asc"},
\code{"median_desc"}, \code{"median"}.  \code{"none"} leaves the levels
as-is.  \code{"mean_asc"} / \code{"mean"} sorts by ascending mean of y.
\code{"mean_desc"} sorts by descending mean.  \code{"median_asc"} /
\code{"median"} sorts by ascending median.  \code{"median_desc"} sorts by
descending median.  Default: \code{"none"}.}

\item{flip}{A logical value.  When \code{TRUE}, the x and y axes are
swapped via \code{coord_flip} and the x-axis factor levels are reversed.
Dimension calculation accounts for the flip.  Default: \code{FALSE}.}

\item{group_by}{A character vector of column names for dodging the points.
Each unique combination becomes a separate dodge group and the points are
offset horizontally via \code{position_jitterdodge} to reduce overlap.
Multiple columns are concatenated with \code{group_by_sep}.  When
\code{NULL} (default), no dodging is applied — only jitter via
\code{position_jitter}.}

\item{group_by_sep}{A character string used to join multiple
\code{group_by} columns.  Default \code{"_"}.}

\item{group_name}{A character string for the dodge-group legend title.
When \code{NULL} (default), the \code{group_by} column name is used.}

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

\item{order_by}{A string expression passed to \code{\link[dplyr]{arrange}()}
to determine which points are labelled.  Evaluated within each x-group
(and facet panel when \code{facet_by} is set).  Default:
\code{"-({y}^2 + {size_by}^2)"}, which selects points farthest from the
origin in y-size radial distance, analogous to VolcanoPlot.}

\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{alpha}{A numeric value in \code{[0, 1]} controlling point
transparency.  Default: \code{1}.}

\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{shape}{A numeric value specifying the point shape (ggplot2 point
shape codes).  Shapes 21–25 are filled shapes with borders; for these
shapes the border behaviour is controlled by \code{border}.  Default:
\code{21} (filled circle).}

\item{border}{Controls the border of points when the shape has a border
(21–25).  If \code{TRUE}, the border colour follows the point fill colour
(same as the group colour).  If a single colour string (e.g.
\code{"black"}), uses that constant border colour for all points.  If
\code{FALSE}, no border is drawn (\code{NA}).  Default: \code{"black"}.}

\item{size_by}{A numeric column name or a single numeric value controlling
point size.  When a column name is provided, sizes are scaled using
\code{scale_size_area(max_size = 6)} and a size legend is shown.  When a
single numeric value, all points use that constant size.  Default:
\code{2}.}

\item{size_name}{A character string for the size legend title.  When
\code{NULL} (default) and \code{size_by} is a column, the column name is
used.  Ignored when \code{size_by} is a single numeric value.}

\item{size_trans}{A function or a function name (as a string) to transform
the \code{size_by} values for size mapping.  The transformed values
determine the point size on the plot, but the legend labels show the
original (untransformed) values.  When \code{NULL} (default), no
transformation is applied.}

\item{y_nbreaks}{A numeric value hinting at the number of break intervals
for the y-axis.  Passed to \code{scale_y_continuous}.  Default: \code{4}.}

\item{jitter_width}{A numeric value controlling the amount of horizontal
jitter (in x-axis units).  Passed to \code{position_jitter} /
\code{position_jitterdodge}.  Default: \code{0.5}.}

\item{jitter_height}{A numeric value controlling the amount of vertical
jitter (in y-axis units).  Passed to \code{position_jitter} /
\code{position_jitterdodge}.  Default: \code{0}.}

\item{y_max, y_min}{Numeric values or quantile strings (e.g. \code{"q95"},
\code{"q5"}) for y-axis limits used in \code{coord_cartesian} /
\code{coord_flip}.  When \code{NULL} (default), the data range is used.
When a quantile string, the corresponding quantile of the y-values is
computed via \code{\link[stats]{quantile}()}.}

\item{y_trans}{A character string specifying a transformation for the
y-axis (e.g. \code{"log10"}, \code{"sqrt"}).  Passed to
\code{\link[ggplot2]{scale_y_continuous}}.  Default: \code{"identity"}.}

\item{add_bg}{A logical value.  When \code{TRUE}, alternating background
stripes are drawn behind the points via \code{\link{bg_layer}()}, using
the x-axis level order.  Default: \code{FALSE}.}

\item{bg_palette}{A character string specifying the palette for the
background stripe colours.  Passed to \code{\link{bg_layer}()}.
Default: \code{"stripe"}.}

\item{bg_palcolor}{A character vector of colours for the background
stripes.  Passed to \code{\link{bg_layer}()}.  When \code{NULL} (default),
colours are derived from \code{bg_palette}.}

\item{bg_alpha}{A numeric value in \code{[0, 1]} for the transparency of
the background stripes.  Default: \code{0.2}.}

\item{add_hline}{One or more numeric values specifying y-values at which
to draw horizontal reference lines.  When \code{NULL} (default), no
reference lines are drawn.}

\item{hline_type}{A character string specifying the line type for the
horizontal reference line(s).  Default: \code{"solid"}.}

\item{hline_width}{A numeric value specifying the line width for the
horizontal reference line(s).  Default: \code{0.5}.}

\item{hline_color}{A character string specifying the colour for the
horizontal reference line(s).  Default: \code{"black"}.}

\item{hline_alpha}{A numeric value in \code{[0, 1]} specifying the alpha
(transparency) for the horizontal reference line(s).  Default: \code{1}.}

\item{labels}{A vector of row names or row indices specifying which points
to label.  When \code{NULL} (default) and \code{nlabel > 0}, the top
\code{nlabel} points per x-group are selected automatically.}

\item{label_by}{A character string naming a column whose values are used
as label text.  When \code{NULL} (default), row names are used as labels.}

\item{nlabel}{An integer specifying the number of points to label per
x-group when \code{labels} is \code{NULL}.  Points are selected by
descending order of \code{order_by}.  Default: \code{5}.  Set to
\code{0} to suppress automatic labelling.}

\item{label_size, label_fg, label_bg, label_bg_r}{Label aesthetics for
\code{\link[ggrepel]{geom_text_repel}}.  \code{label_size}: text size
(default \code{3}).  \code{label_fg}: text colour (default
\code{"black"}).  \code{label_bg}: background (halo) colour for the label
text (default \code{"white"}).  \code{label_bg_r}: background border
radius (default \code{0.1}).}

\item{highlight}{A specification of which points to highlight.  Can be:
\code{TRUE} (highlight all points), a numeric vector of row indices, a
single character string parsed as an \R expression, or a character vector
of row names.  When a point is highlighted, an overlay \code{geom_point}
is drawn on top with \code{highlight_color}, \code{highlight_size}, and
\code{highlight_alpha}.  Default: \code{NULL} (no highlighting).}

\item{highlight_color}{A character string specifying the colour of
highlighted points.  Default: \code{"red2"}.}

\item{highlight_size}{A numeric value specifying the size of highlighted
points.  Default: \code{1}.}

\item{highlight_alpha}{A numeric value in \code{[0, 1]} specifying the
transparency of highlighted points.  Default: \code{1}.}

\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.  Passed to
\code{\link{validate_common_args}()}.  Default: \code{8525}.}

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

\item{ncol, nrow}{Integer number of columns / rows for the combined layout
(passed to \code{\link[patchwork]{wrap_plots}}).}

\item{byrow}{Logical; fill the combined layout by row.  Default
\code{TRUE} (passed to \code{\link[patchwork]{wrap_plots}}).}

\item{axes}{A character string specifying how axes should be treated
across the combined layout (passed to \code{\link[patchwork]{wrap_plots}}).}

\item{axis_titles}{A character string specifying how axis titles should be
treated across the combined layout.  Defaults to \code{axes}.}

\item{guides}{A character string specifying how guides (legends) should be
collected across panels (passed to \code{\link{combine_plots}()}).}

\item{design}{A custom layout design for the combined plot (passed to
\code{\link{combine_plots}()}).}

\item{...}{Additional arguments.}
}
\value{
A \code{ggplot} object (when \code{split_by} is \code{NULL}), a
\code{patchwork} object (when \code{split_by} is provided and
\code{combine = TRUE}), or a named list of \code{ggplot} objects (when
\code{combine = FALSE}).  All \code{ggplot} objects have \code{height}
and \code{width} attributes in inches.
}
\description{
Draws a jittered point plot showing the distribution of numeric y-values
across a discrete x-axis.  Each data point is rendered with random jitter
along the x-axis (and optionally the y-axis) to reduce overplotting, making
it easy to visualise data density, spread, and outliers within each category.

The function supports \strong{x-axis reordering} by y-value summaries
(mean or median), \strong{group dodging} via \code{group_by} to compare
subgroups side-by-side, \strong{point labelling} with automatic top-n
selection using a configurable distance metric (default: radial distance
\code{y^2 + size^2}), \strong{point highlighting} for emphasis, optional
\strong{horizontal reference lines}, and \strong{wide-format input} via
\code{in_form}.  Colour control, faceting, and splitting into separate
sub-plots via \code{split_by} are supported.
}
\section{split_by workflow}{

When \code{split_by} is provided:
\enumerate{
\item \code{\link{validate_common_args}()} validates the \code{seed}.
\item \code{\link{check_keep_na}()} and \code{\link{check_keep_empty}()}
normalise the \code{keep_na} / \code{keep_empty} arguments for all
relevant columns (\code{x}, \code{split_by}, \code{group_by},
\code{facet_by}).
\item The \code{split_by} column is validated via
\code{\link{check_columns}()} with \code{force_factor = TRUE}.
Multiple \code{split_by} columns are concatenated with
\code{split_by_sep}.
\item If \code{split_by} is not \code{NULL}, the data frame is split
(preserving factor 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
via \code{\link{check_palette}()}, \code{\link{check_palcolor}()},
and \code{\link{check_legend}()}.
\item \code{\link{JitterPlotAtomic}()} is called for each split.  If
\code{title} is a function, it receives the split level name and
can generate dynamic titles.
\item Results are combined via \code{\link{combine_plots}()} (when
\code{combine = TRUE}) or returned as a named list.
}
}

\examples{
\donttest{
set.seed(8525)
n <- 180
x <- factor(
    sample(c("A", NA, LETTERS[3:5]), n, replace = TRUE),
    levels = c("A", "B", "C", "D", "E")
)
group <- factor(
    sample(c("G1", NA, "G3"), n, replace = TRUE),
    levels = c("G1", "G2", "G3")
)
size <- rexp(n, rate = 1)
id <- paste0("pt", seq_len(n))
y <- rnorm(n, mean = ifelse(is.na(group), 0, ifelse(group == "G1", 0.5, -0.5))) +
     as.numeric(ifelse(is.na(x), 0, x))/10
df <- data.frame(
  x = x,
  y = y,
  group = group,
  size = size,
  id = id
)

# Basic
JitterPlot(df, x = "x", y = "y")

# Keep empty x levels and NA
JitterPlot(df, x = "x", y = "y", keep_na = TRUE, keep_empty = TRUE)

# Map size with transform; legend shows original values
JitterPlot(df, x = "x", y = "y", size_by = "size", size_name = "Abundance",
    size_trans = sqrt, order_by = "-y^2")

# Dodge by group and add a horizontal line
JitterPlot(df, x = "x", y = "y", group_by = "group",
  add_hline = 0, hline_type = "dashed", hline_color = "red2")

# Keep the empty levels only for color coding
# Note the G3 is not blue (which is taken by unused level G2)
JitterPlot(df, x = "x", y = "y", group_by = "group",
    keep_na = TRUE, keep_empty = 'level')

# Label top points by distance (y^2 + size^2)
JitterPlot(df, x = "x", y = "y", size_by = "size", label_by = "id", nlabel = 3)

# Flip axes
JitterPlot(df, x = "x", y = "y", flip = TRUE)
}
}
