% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/lineplot.R
\name{LinePlot}
\alias{LinePlot}
\title{Line plot}
\usage{
LinePlot(
  data,
  x,
  y = NULL,
  group_by = NULL,
  group_by_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  fill_point_by_x_if_no_group = TRUE,
  color_line_by_x_if_no_group = TRUE,
  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,
  keep_na = FALSE,
  keep_empty = FALSE,
  line_type = "solid",
  line_width = 1,
  line_alpha = 0.8,
  add_hline = FALSE,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  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",
  facet_by = NULL,
  facet_scales = "fixed",
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  facet_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  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{y}{A character string specifying the column name of the data frame to plot for the y-axis.}

\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{split_by}{A character vector of column names to split the data by.
Each split level produces a separate sub-plot. Multiple columns are
concatenated with \code{split_by_sep}.}

\item{split_by_sep}{A character string used to join multiple
\code{split_by} column values. Default \code{"_"}.}

\item{fill_point_by_x_if_no_group}{A logical value. When TRUE (default),
points are filled by the x-axis categories via the palette when
\code{group_by = NULL}. Passed to \code{LinePlotSingle} as
\code{fill_point_by_x}. Has no effect when \code{group_by} is set.}

\item{color_line_by_x_if_no_group}{A logical value. When TRUE (default),
lines are coloured by the x-axis categories via the palette when
\code{group_by = NULL}. Passed to \code{LinePlotSingle} as
\code{color_line_by_x}. Has no effect when \code{group_by} is set.}

\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{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{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{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{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{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{combine}{Logical; when TRUE (default), per-split plots are combined
into a single \code{patchwork} object. When FALSE, a named list of
\code{ggplot} objects is returned.}

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

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

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

\item{facet_args}{A list of additional arguments passed to
\code{\link{facet_plot}()} for fine-grained control over faceting
(e.g. \code{scales}, \code{space}, \code{labeller}).}

\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 8525.}

\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 should be
collected across panels. Passed to \code{\link{combine_plots}()}.}

\item{design}{A custom layout specification for combined plots (passed
to \code{\link{combine_plots}()}). Overrides \code{nrow}/\code{ncol}
when specified.}

\item{...}{Additional arguments.}
}
\value{
A \code{ggplot} object, a \code{patchwork} object (when
\code{combine = TRUE} with \code{split_by}), or a named list of
\code{ggplot} objects (when \code{combine = FALSE}), each with
\code{height} and \code{width} attributes in inches.
}
\description{
Draws a line plot showing the change of a numeric value across the
progression of a categorical x-axis variable.  Each x-axis category is
rendered as a point connected by a line, with support for multiple
grouped series, error bars, highlighted points, background stripes,
and a horizontal reference line.

Key features:
\itemize{
\item \strong{Colour modes:} lines and points can be coloured by x
category (single-series) or by a \code{group_by} variable
(multi-series), or use a single uniform colour.
\item \strong{Error bars:} additive error bars via
\code{errorbar_sd}, \code{errorbar_min}, or \code{errorbar_max}.
\item \strong{Highlighting:} specific points can be emphasised with a
different colour and size via indices, row names, or a filter
expression.
\item \strong{Background stripes:} \code{add_bg = TRUE} draws
alternating bands for visual grouping.
\item \strong{Count aggregation:} omit \code{y} to plot observation
counts per x category.
}
}
\section{split_by Workflow}{

When \code{split_by} is provided:
\enumerate{
\item \strong{Column validation} -- \code{\link{check_columns}()}
resolves \code{split_by} with multi-column concatenation.
\item \strong{NA / empty pre-processing} --
\code{\link{process_keep_na_empty}()} handles \code{keep_na} /
\code{keep_empty} for the split column before splitting, then
removes the split column from the per-split lists.
\item \strong{Data splitting} -- splits \code{data} by
\code{split_by} levels, preserving factor level order.  When
\code{split_by = NULL}, the data is wrapped in a single-element
list with name \code{"..."}.
\item \strong{Per-split palette / colour} --
\code{\link{check_palette}()} and \code{\link{check_palcolor}()}
resolve per-split palette and colour overrides.
\item \strong{Per-split legend} -- \code{\link{check_legend}()}
resolves \code{legend.position} and \code{legend.direction} per
split level.
\item \strong{Per-split title} -- when \code{title} is a function, it
receives the default title (the split level name) and can return
a custom string; otherwise \code{title \%||\% split_level} is
used.
\item \strong{Dispatch} -- each split subset is passed to
\code{\link{LinePlotAtomic}}.
\item \strong{Combination} -- \code{\link{combine_plots}()} assembles
the list of plots via \code{patchwork::wrap_plots}, honouring
\code{nrow}/\code{ncol}/\code{byrow}/\code{design}.
}
}

\examples{
\donttest{
data <- data.frame(
   x = factor(c("A", "B", "C", "D", "A", "B", "C", "D"), levels = LETTERS[1:6]),
   y = c(10, 8, 16, 4, 6, 12, 14, 2),
   group = c("G1", "G1", "G1", "G1", "G2", "G2", "G2", "G2"),
   facet = c("F1", "F1", "F2", "F2", "F3", "F3", "F4", "F4")
)

# --- Basic usage ---
LinePlot(data, x = "x", y = "y")
LinePlot(data, x = "x", y = "y", highlight = "group == 'G1'",
   fill_point_by_x_if_no_group = FALSE, color_line_by_x_if_no_group = FALSE)

# --- Grouped lines ---
LinePlot(data, x = "x", y = "y", group_by = "group")
LinePlot(data, x = "x", y = "y", group_by = "group",
   add_hline = 10, hline_color = "red")
LinePlot(data, x = "x", y = "y", group_by = "group", add_bg = TRUE,
   highlight = "y > 10")
LinePlot(data, x = "x", y = "y", group_by = "group", facet_by = "facet")
LinePlot(data, x = "x", y = "y", group_by = "group", split_by = "facet")

# --- Per-split styling ---
LinePlot(data, x = "x", y = "y", split_by = "group",
         palcolor = list(G1 = c("red", "blue"), G2 = c("green", "black")))

# --- keep_na and keep_empty ---
data <- data.frame(
   x = factor(c("A", "B", NA, "D", "A", "B", NA, "D"), levels = LETTERS[1:4]),
   y = c(10, 8, 16, 4, 6, 12, 14, 2),
   group = factor(c("G1", "G1", "G1", NA, NA, "G3", "G3", "G3"),
     levels = c("G1", "G2", "G3")),
   facet = c("F1", "F1", "F2", "F2", "F3", "F3", "F4", "F4")
)

LinePlot(data, x = "x", y = "y", keep_na = TRUE)
LinePlot(data, x = "x", y = "y", keep_empty = TRUE)
LinePlot(data, x = "x", y = "y", keep_empty = 'level')
LinePlot(data, x = "x", y = "y", group_by = "group", keep_na = TRUE)
LinePlot(data, x = "x", y = "y", group_by = "group", keep_empty = TRUE)
LinePlot(data, x = "x", y = "y", group_by = "group",
   keep_empty = list(x = TRUE, group = 'level'))
}
}
