% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/trendplot.R
\name{TrendPlotAtomic}
\alias{TrendPlotAtomic}
\title{Atomic trend plot (internal)}
\usage{
TrendPlotAtomic(
  data,
  x,
  y = NULL,
  x_sep = "_",
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  scale_y = FALSE,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  x_text_angle = 0,
  aspect.ratio = 1,
  legend.position = waiver(),
  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 to plot on the
x-axis. Must be character or factor. Multiple columns can be provided;
they are concatenated with \code{x_sep} as the separator.}

\item{y}{A character string specifying the numeric column for the y-axis.
When \code{NULL}, the count of observations in each (\code{x},
\code{group_by}, \code{facet_by}) combination is used.}

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

\item{group_by}{A character vector of column names to fill the bars and
areas by. Each unique combination becomes a separate stacked segment.
Multiple columns are concatenated with \code{group_by_sep}. When
\code{NULL}, a single filled bar/area is drawn and the legend is hidden.}

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

\item{group_name}{A character string used as the fill legend title.
When \code{NULL}, the \code{group_by} column name is used.}

\item{scale_y}{A logical value. When \code{TRUE}, y-values are scaled to
proportions within each (\code{x}, \code{facet_by}) group so that each
x position stacks to 1.0. The y-axis labels switch from numeric to
percent format automatically.}

\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 specifying the transparency of the plot.}

\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{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) attached.
}
\description{
Core implementation for drawing a single trend plot. This is the workhorse
behind the exported \code{\link{TrendPlot}} function -- it takes a \strong{single}
data frame (no \code{split_by} support) and returns a \code{ggplot} object.
A trend plot combines stacked bars (\code{\link[ggplot2]{geom_col}()}) with
a semi-transparent area background (\code{\link[ggplot2]{geom_area}()}) to
show how one or more groups accumulate across a discrete x-axis. This hybrid
style sits between a bar plot and an area plot, preserving the discrete
category separation of bars while softening the visual with an area fill.

The function supports count aggregation (omit \code{y} to plot observation
counts per x-category), proportion scaling (\code{scale_y = TRUE} normalises
each x position to 100\\%), per-group colour control, and faceting.
}
\section{Architecture}{

\enumerate{
\item \strong{Column resolution} -- \code{x}, \code{y}, \code{group_by},
and \code{facet_by} are validated and transformed via
\code{\link{check_columns}}. Multi-column inputs for \code{x} and
\code{group_by} are concatenated into single columns using their
respective separators (\code{x_sep}, \code{group_by_sep}).
\item \strong{Count aggregation} -- when \code{y = NULL}, the count of
observations in each unique (\code{x}, \code{group_by},
\code{facet_by}) combination is computed as a new \code{.count}
column. Factor levels are preserved after aggregation.
\item \strong{Proportion scaling} -- when \code{scale_y = TRUE}, the
y-values are divided by the sum within each (\code{x},
\code{facet_by}) group, producing a proportion (0--1). Percent
labels are used automatically on the y-axis.
\item \strong{NA / empty-level handling} --
\code{\link{process_keep_na_empty}()} applies \code{keep_na} and
\code{keep_empty} policies. Per-column \code{keep_empty} settings
are extracted for \code{x}, \code{group_by}, and \code{facet_by}
independently. The facet columns must have identical
\code{keep_empty} values. Note that \code{keep_empty = TRUE} is
not supported globally because empty categories would break the
continuity of the x-axis.
\item \strong{Group fill setup} -- when \code{group_by = NULL}, a dummy
\code{.fill} factor is created so the single group still draws with
the first palette colour. The legend is suppressed
(\code{legend.position = "none"}).
\item \strong{Data completion} -- \code{\link[tidyr]{complete}()} pads
all \code{x} by \code{group_by} (by \code{facet_by})
combinations with \code{y = 0}. This prevents
\code{\link[ggplot2]{geom_area}()} from interpolating across missing
groups, which would otherwise cause stacked areas to exceed the
correct total.
\item \strong{Area layer construction} -- the completed data is expanded
by duplicating each row and offsetting the x-axis positions by
\eqn{\pm 0.2} on a numeric scale, creating discrete-width area
strips that align perfectly with the bars.
\item \strong{Colour mapping} -- \code{\link{palette_this}()} assigns
colours to all \code{group_by} levels, including \code{NA}
(defaulting to \code{"grey80"}).
\item \strong{Plot assembly} -- the \code{ggplot} object is built with
\code{geom_area()} (at half \code{alpha}, grey outline) as a
background fill, overlaid with \code{geom_col()} (full \code{alpha},
black outline, width 0.4) as the foreground bars. Both layers use
\code{position_stack(vjust = 0.5)}. The x-axis uses
\code{scale_x_discrete()} and the y-axis uses
\code{scale_y_continuous()} (percent labels when scaled). The
fill scale \code{drop} argument is controlled by
\code{keep_empty_group}.
\item \strong{Dimension calculation} --
\code{\link{calculate_plot_dimensions}()} computes plot height and
width from the x-axis category count, \code{aspect.ratio}, and
legend metrics. The base height increases for plots with 10 or more
x categories (from 4.5 to 6.5 inches). The resulting \code{height}
and \code{width} attributes are stored on the \code{ggplot} object.
\item \strong{Faceting} -- \code{\link{facet_plot}()} wraps the plot with
\code{facet_wrap} / \code{facet_grid} if \code{facet_by} is
provided, respecting the \code{keep_empty} setting for facet
variables.
}
}

\keyword{internal}
