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Atomic line-plot dispatcher (internal)

Source: R/lineplot.R
LinePlotAtomic.Rd

Dispatcher that routes to LinePlotSingle or LinePlotGrouped depending on whether group_by is provided. Handles faceting via facet_plot() after the base plot is built.

Usage

LinePlotAtomic(
  data,
  x,
  y = NULL,
  group_by = NULL,
  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,
  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,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_args = list(),
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  ...
)

Arguments

data

A data frame.

x

A character string specifying the column name for the x-axis. Must be character or factor.

y

A character string specifying the numeric column for the y-axis.

group_by

A character vector of column names to group the data by. When NULL, a single-series line plot is drawn via LinePlotSingle. When provided, a multi-series line plot is drawn via LinePlotGrouped.

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 group_by = NULL. Passed to LinePlotSingle as fill_point_by_x. Has no effect when group_by is set.

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 group_by = NULL. Passed to LinePlotSingle as color_line_by_x. Has no effect when group_by is set.

add_bg

A logical value. When TRUE, alternating background stripes are drawn via bg_layer(). Default FALSE.

bg_palette

A character string specifying the palette for the background stripe colours. Default "stripe".

bg_palcolor

A character vector of colours for the background stripes. When NULL (default), colours are derived from bg_palette.

bg_alpha

A numeric value in [0, 1] for the transparency of background stripes. Default 0.2.

add_errorbars

A logical value. When TRUE, error bars are added via geom_errorbar(). Requires errorbar_sd or errorbar_min/errorbar_max. Default FALSE.

errorbar_width

A numeric value for the width of the error bar caps. Default 0.1.

errorbar_alpha

A numeric value in [0, 1] for the transparency of error bars. Default 1.

errorbar_color

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

errorbar_linewidth

A numeric value for the line width of error bars. Default 0.75.

errorbar_min

A character string naming the column with the lower error bar bound. Ignored when errorbar_sd is provided.

errorbar_max

A character string naming the column with the upper error bar bound. Ignored when errorbar_sd is provided.

errorbar_sd

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

highlight

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

highlight_size

A numeric value for the size of highlighted points. Defaults to pt_size - 0.75.

highlight_color

A character string for the colour of highlighted points. Default "red2".

highlight_alpha

A numeric value in [0, 1] for the transparency of highlighted points. Default 0.8.

pt_alpha

A numeric value in [0, 1] for the transparency of points. Default 1.

pt_size

A numeric value for the point size. Default 5.

add_hline

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

hline_type

A character string specifying the line type of the horizontal reference line. Default "solid".

hline_width

A numeric value for the width of the horizontal reference line. Default 0.5.

hline_color

A character string for the colour of the horizontal reference line. Default "black".

hline_alpha

A numeric value in [0, 1] for the transparency of the horizontal reference line. Default 1.

line_type

A character string specifying the line type. Default "solid".

line_width

A numeric value for the line width (in mm). Default 1.

line_alpha

A numeric value in [0, 1] for the transparency of the line. Default 0.8.

theme

A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".

theme_args

A list of arguments to pass to the theme function.

palette

A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.

palcolor

A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).

palreverse

A logical value indicating whether to reverse the palette. Default is FALSE.

x_text_angle

A numeric value specifying the angle of the x-axis text.

aspect.ratio

A numeric value specifying the aspect ratio of the plot.

legend.position

A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".

legend.direction

A character string specifying the direction of the legend.

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.

subtitle

A character string specifying the subtitle of the plot.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

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 x, group_by, fill_by, etc.

  • FALSE (default): Drop empty factor levels from the data before plotting.

  • TRUE: Keep empty factor levels and show them as a separate category in the plot.

  • "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: levels

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 x, group_by, fill_by, etc.

facet_by

A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by split_by and generate multiple plots and combine them into one using patchwork::wrap_plots

facet_scales

Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See ggplot2::facet_wrap

facet_args

A list of additional arguments passed to facet_plot() for fine-grained control over faceting (e.g. scales, space, labeller).

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.

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.

facet_byrow

A logical value indicating whether to fill the plots by row. Default is TRUE.

...

Additional arguments.

Value

A ggplot object with height and width attributes (in inches).

Dispatch Logic

  1. Column resolution – facet_by is validated via check_columns.

  2. Routing – when group_by = NULL, delegates to LinePlotSingle (ungrouped, single-series line plot). When group_by is provided, delegates to LinePlotGrouped (multi-series line plot).

  3. Facet keep_empty consistency – when facet_by contains multiple columns, their keep_empty values must be identical.

  4. Faceting – facet_plot() applies facet_wrap / facet_grid with the resolved drop argument (derived from keep_empty).