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Atomic bar plot (internal)

Source: R/barplot.R
BarPlotAtomic.Rd

Dispatcher that routes to BarPlotSingle (when group_by = NULL) or BarPlotGrouped (when group_by is provided). This is the core implementation layer — it takes a single data frame (no split_by support) and returns a ggplot object with faceting applied.

Usage

BarPlotAtomic(
  data,
  x,
  x_sep = "_",
  y = NULL,
  scale_y = FALSE,
  flip = FALSE,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  fill_by = TRUE,
  fill_name = NULL,
  label_nudge = 0.02,
  label = NULL,
  label_fg = "black",
  label_size = 4,
  label_bg = "white",
  label_bg_r = 0.1,
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  theme = "theme_this",
  theme_args = list(),
  palette = NULL,
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  lower_quantile = 0,
  upper_quantile = 0.99,
  lower_cutoff = NULL,
  upper_cutoff = NULL,
  x_text_angle = 0,
  aspect.ratio = 1,
  add_line = NULL,
  line_color = "red2",
  line_width = 0.6,
  line_type = 2,
  line_name = NULL,
  add_trend = FALSE,
  trend_color = "black",
  trend_linewidth = 1,
  trend_ptsize = 2,
  position = "auto",
  position_dodge_preserve = "total",
  y_min = NULL,
  y_max = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  keep_na = FALSE,
  keep_empty = FALSE,
  expand = waiver(),
  width = waiver(),
  facet_by = NULL,
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  facet_args = list(),
  ...
)

Arguments

data

A data frame.

x

A character string specifying the column name of the data frame to plot for the x-axis.

x_sep

A character string to join multiple x columns. Default "_".

y

A character string specifying the column name of the data frame to plot for the y-axis.

scale_y

A logical value. When TRUE, y-values are scaled to proportions within each x position so that each position's total is 100\ Only applicable when position = "stack".

flip

Logical; if TRUE, swap the x and y axes.

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 group_by_sep as the separator

group_by_sep

The separator for multiple group_by columns. See group_by

group_name

A character string for the group fill legend title. When NULL, the group_by column name is used.

fill_by

A variable used to fill the bars. Both categorical and numeric columns are accepted:

  • TRUE (default) — fill by the x-axis values.

  • FALSE — solid fill (first palette colour).

  • A column name (character/factor) — discrete colour scale.

  • A column name (numeric) — continuous gradient with quantile / cutoff controls.

Ignored when group_by is provided (fill is determined by group_by).

fill_name

A character string for the fill legend title. Only applies when group_by = NULL and the fill is from fill_by.

label_nudge

A numeric value controlling the distance between labels and the bar top, expressed as a fraction of the data range.

label

A column name (or TRUE) for text labels on bars. When TRUE, the y-axis values are labelled. When a column name, the values in that column are used.

label_fg

A character string specifying the label text colour.

label_size

A numeric value specifying the label text size.

label_bg

A character string specifying the label background colour.

label_bg_r

A numeric value specifying the label background corner radius.

add_bg

Logical; add alternating background stripes behind the bars.

bg_palette

Palette for the background stripes.

bg_palcolor

Custom colours for the background stripes.

bg_alpha

Alpha transparency for the background stripes.

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.

alpha

A numeric value specifying the transparency of the plot.

lower_quantile, upper_quantile

Lower and upper quantiles for the continuous color/fill scale. The actual cutoffs are determined by these quantiles when lower_cutoff and upper_cutoff are NULL. Defaults: lower_quantile = 0, upper_quantile = 0.99.

lower_cutoff, upper_cutoff

Explicit lower and upper cutoffs for the continuous color/fill scale. When NULL (the default), the cutoffs are determined by lower_quantile and upper_quantile via quantile. Values outside the [lower_cutoff, upper_cutoff] range are clamped (winsorized) to the nearest cutoff value.

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.

add_line

A numeric y-intercept for a horizontal reference line.

line_color

Colour of the reference line.

line_width

Width of the reference line.

line_type

Linetype of the reference line (e.g., 1 = solid, 2 = dashed).

line_name

Legend name for the reference line.

add_trend

Logical; add a trend line and points connecting the bar tops.

trend_color

Colour of the trend line.

trend_linewidth

Width of the trend line.

trend_ptsize

Size of the trend line points.

position

A character string specifying the bar layout: "auto" (default: dodge when \(\le\)5 groups, stack otherwise), "dodge" (side-by-side), or "stack" (stacked on top of each other).

position_dodge_preserve

A character string passed to position_dodge2(): "total" preserves the overall bar group width; "single" preserves individual bar widths.

y_min, y_max

Numeric limits for the y-axis (or x-axis when flipped).

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_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.

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

expand

The values to expand the x and y axes. It is like CSS padding. When a single value is provided, it is used for both axes on both sides. When two values are provided, the first value is used for the top/bottom side and the second value is used for the left/right side. When three values are provided, the first value is used for the top side, the second value is used for the left/right side, and the third value is used for the bottom side. When four values are provided, the values are used for the top, right, bottom, and left sides, respectively. You can also use a named vector to specify the values for each side. When the axis is discrete, the values will be applied as 'add' to the 'expansion' function. When the axis is continuous, the values will be applied as 'mult' to the 'expansion' function. See also https://ggplot2.tidyverse.org/reference/expansion.html

width

A numeric value specifying the bar width (0–1).

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_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.

facet_args

A list of additional arguments passed to the faceting function (e.g., scales, labeller).

...

Additional arguments.

Value

A ggplot object, possibly faceted, with height and width attributes (in inches) attached.

Dispatch logic

  • Without group_by — delegates to BarPlotSingle. fill_by controls bar colouring: TRUE (default) fills by x-axis values, FALSE uses a single colour, a character column produces discrete colours, and a numeric column produces a continuous gradient.

  • With group_by — delegates to BarPlotGrouped. fill_by must match group_by or be left as default; an explicit mismatch raises a stop error. position controls dodge vs. stack layout with automatic selection based on group count (\(\le\)5 → dodge, >5 → stack).

After the delegate returns, facet_plot() wraps the result with facet_wrap / facet_grid if facet_by is provided.