% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/lineplot.R
\name{LinePlotGrouped}
\alias{LinePlotGrouped}
\title{Multi-series line plot (internal)}
\usage{
LinePlotGrouped(
  data,
  x,
  y = NULL,
  group_by,
  group_by_sep = "_",
  facet_by = NULL,
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_errorbars = FALSE,
  errorbar_width = 0.1,
  errorbar_alpha = 1,
  errorbar_color = "grey30",
  errorbar_linewidth = 0.75,
  errorbar_min = NULL,
  errorbar_max = NULL,
  errorbar_sd = NULL,
  highlight = NULL,
  highlight_size = pt_size - 0.75,
  highlight_color = "red2",
  highlight_alpha = 0.8,
  pt_alpha = 1,
  pt_size = 5,
  add_hline = FALSE,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  line_type = "solid",
  line_width = 1,
  line_alpha = 0.8,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  x_text_angle = 0,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  keep_empty = FALSE,
  keep_na = FALSE,
  ...
)
}
\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{y}{A character string specifying the column name of the data frame to plot for the y-axis.}

\item{group_by}{A character vector of column names to group the data by.
Each unique combination becomes a separate line. Multiple columns are
concatenated with \code{group_by_sep}. When \code{NULL}, the
\code{LinePlotSingle} path is used instead.}

\item{group_by_sep}{A character string used to join multiple
\code{group_by} column values into a single group identifier. Default
\code{"_"}.}

\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{add_bg}{A logical value. When TRUE, alternating background stripes
are drawn via \code{\link{bg_layer}()}. Default FALSE.}

\item{bg_palette}{A character string specifying the palette for the
background stripe colours. Default \code{"stripe"}.}

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

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

\item{add_errorbars}{A logical value. When TRUE, error bars are added via
\code{\link[ggplot2]{geom_errorbar}()}. Requires \code{errorbar_sd} or
\code{errorbar_min}/\code{errorbar_max}. Default FALSE.}

\item{errorbar_width}{A numeric value for the width of the error bar
caps. Default 0.1.}

\item{errorbar_alpha}{A numeric value in \code{[0, 1]} for the transparency of
error bars. Default 1.}

\item{errorbar_color}{A character string for the colour of the error
bars. When \code{"line"}, error bars are coloured the same as the lines
(by x when \code{color_line_by_x = TRUE}, or single colour otherwise).
Default \code{"grey30"}.}

\item{errorbar_linewidth}{A numeric value for the line width of error
bars. Default 0.75.}

\item{errorbar_min}{A character string naming the column with the lower
error bar bound. Ignored when \code{errorbar_sd} is provided.}

\item{errorbar_max}{A character string naming the column with the upper
error bar bound. Ignored when \code{errorbar_sd} is provided.}

\item{errorbar_sd}{A character string naming the column with the standard
deviation. When \code{errorbar_min} and \code{errorbar_max} are not
provided, error bars are computed as y +/- \code{errorbar_sd}.}

\item{highlight}{A vector of row indices, row names, a single string
expression (e.g. \code{"y > 10"}) filtering rows to highlight, or TRUE
to highlight all points. When NULL (default), no highlighting is
applied.}

\item{highlight_size}{A numeric value for the size of highlighted points.
Defaults to \code{pt_size - 0.75}.}

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

\item{highlight_alpha}{A numeric value in \code{[0, 1]} for the transparency of
highlighted points. Default 0.8.}

\item{pt_alpha}{A numeric value in \code{[0, 1]} for the transparency of points.
Default 1.}

\item{pt_size}{A numeric value for the point size. Default 5.}

\item{add_hline}{A numeric value specifying the y-intercept of a
horizontal reference line. When FALSE (default), no line is drawn.}

\item{hline_type}{A character string specifying the line type of the
horizontal reference line. Default \code{"solid"}.}

\item{hline_width}{A numeric value for the width of the horizontal
reference line. Default 0.5.}

\item{hline_color}{A character string for the colour of the horizontal
reference line. Default \code{"black"}.}

\item{hline_alpha}{A numeric value in \code{[0, 1]} for the transparency of the
horizontal reference line. Default 1.}

\item{line_type}{A character string specifying the line type. Default
\code{"solid"}.}

\item{line_width}{A numeric value for the line width (in mm). Default 1.}

\item{line_alpha}{A numeric value in \code{[0, 1]} for the transparency of the
line. Default 0.8.}

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

\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{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{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{...}{Additional arguments.}
}
\value{
A \code{ggplot} object with \code{height} and \code{width}
attributes (in inches).
}
\description{
Core implementation for drawing a multi-series line plot.  This is the
workhorse behind \code{\link{LinePlotAtomic}} for grouped data -- it takes a
\strong{single} data frame with a \code{group_by} column and returns a
\code{ggplot} object.  Each group receives its own line rendered in a
distinct colour from the palette, with optional error bars, highlighted
points, per-group horizontal reference lines, and background stripes.
}
\section{Architecture}{

\enumerate{
\item \strong{ggplot dispatch} -- selects \code{gglogger::ggplot} or
\code{ggplot2::ggplot} based on
\code{getOption("plotthis.gglogger.enabled")}.
\item \strong{Column resolution} -- \code{x} (forced to factor),
\code{y}, \code{group_by} (multi-column concatenation supported),
and \code{facet_by} are validated via
\code{\link{check_columns}}.
\item \strong{Count aggregation} -- when \code{y = NULL}, the count of
observations per (\code{x}, \code{group_by}, \code{facet_by})
combination is computed and used as \code{y}.
\item \strong{Error bar validation} -- if \code{add_errorbars = TRUE},
checks that either \code{errorbar_min}/\code{errorbar_max} or
\code{errorbar_sd} is provided.
\item \strong{NA / empty-level handling} --
\code{\link{process_keep_na_empty}()} applies \code{keep_na} and
\code{keep_empty} policies.
\item \strong{Highlight parsing} -- \code{highlight} (indices, row
names, expression string, or \code{TRUE}) is resolved to a subset
of data rows.
\item \strong{Background layer} -- when \code{add_bg = TRUE},
alternating background stripes are drawn via
\code{\link{bg_layer}()}.
\item \strong{Colour assignment} -- \code{\link{palette_this}()}
assigns colours to all \code{group_by} levels (including
\code{NA}, defaulting to \code{"grey80"}).
\item \strong{Horizontal reference line} -- when \code{add_hline} is
set, one or more \code{geom_hline()} are added.  If
\code{hline_color = TRUE}, each horizontal line is coloured to
match the corresponding group colour, and \code{add_hline} can
be a named vector/ list mapping groups to intercept values.
\item \strong{Line rendering} -- lines are coloured and grouped by
\code{group_by} via \code{\link[ggplot2]{geom_line}()} with
\code{aes(color = group_by, group = group_by)} and
\code{scale_color_manual()}.
\item \strong{Error bars} -- when \code{add_errorbars = TRUE}, three
colour modes are supported: follow the line colour
(\code{"line"}), track \code{group_by} colours, or use a
constant colour.  Error bars are added via
\code{\link[ggplot2]{geom_errorbar}()}.
\item \strong{Point rendering} -- points are filled per group via
\code{\link[ggplot2]{geom_point}()} with
\code{aes(fill = group_by)} and \code{scale_fill_manual()}.
\item \strong{Highlight overlay} -- an additional \code{geom_point()}
layer draws highlighted rows in the specified colour and size.
\item \strong{Plot assembly} -- \code{scale_x_discrete()},
\code{labs()}, theme application, axis styling (angle, grid
lines), and legend positioning.
\item \strong{Dimension calculation} --
\code{\link{calculate_plot_dimensions}()} computes \code{height}
and \code{width} attributes (in inches) from x-axis category
count, aspect ratio, and legend metrics (legend entries reflect
group levels rather than x levels).
}
}

\keyword{internal}
