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Atomic ridge plot

Source: R/densityplot.R
RidgePlotAtomic.Rd

Core implementation for ridge (joy) plots. Renders overlapping density curves for each group on the y-axis using ggridges::geom_density_ridges(), with optional vertical reference lines and wide-to-long data conversion.

The function accepts data in two forms:

  • long form (default) — a numeric x column plus a group_by factor column whose levels become the y-axis ridges.

  • wide form — multiple numeric columns named in group_by are gathered via tidyr::pivot_longer() into .x / .group columns, then processed identically to the long form.

Vertical reference lines (add_vline) can be specified as a numeric vector (same lines for all groups), a named list (per-group values), or TRUE (group means). When vline_color = TRUE, each line is coloured with a darkened blend of the corresponding ridge fill.

Usage

RidgePlotAtomic(
  data,
  x = NULL,
  in_form = c("long", "wide"),
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  add_vline = NULL,
  vline_type = "solid",
  vline_color = TRUE,
  vline_width = 0.5,
  vline_alpha = 1,
  flip = FALSE,
  alpha = 0.8,
  scale = NULL,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  x_text_angle = 90,
  keep_na = FALSE,
  keep_empty = FALSE,
  reverse = FALSE,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = "none",
  legend.direction = "vertical",
  ...
)

Arguments

data

A data frame. Accepted in two forms:

  • long (in_form = "long"): a numeric column (named by x) and a factor column (named by group_by) whose levels become y-axis ridges.

  • wide (in_form = "wide"): multiple numeric columns listed in group_by are gathered into .x / .group via tidyr::pivot_longer().

x

A character string specifying the column name for the numeric values plotted on the x-axis. When in_form = "wide", x should be NULL; the gathered values are stored in a synthetic .x column.

in_form

A character string specifying whether data is in "long" (default) or "wide" format.

group_by

A character string specifying the column(s) whose levels define the individual ridges on the y-axis. Multiple columns are concatenated with group_by_sep. In wide mode, these are the column names to gather.

group_by_sep

A character string used to join multiple group_by column values into a single factor level. In wide form the columns are not concatenated (each becomes its own ridge). Default: "_".

group_name

A character string used as the legend title for the group_by fill aesthetic. Defaults to the (concatenated) group_by column name.

add_vline

A specification for vertical reference lines:

  • NULL or FALSE: no lines.

  • TRUE: draw a line at the mean of each group.

  • A numeric vector: draw the same lines for all groups.

  • A named list of numeric vectors: per-group lines, where names should match group_by levels.

vline_type

A character string specifying the line type for the vertical reference lines. Passed as linetype to geom_vline(). Default: "solid".

vline_color

The colour of the vertical reference lines:

  • A literal colour value or vector (recycled): applied directly.

  • TRUE (default): each line is coloured with a darkened blend of the corresponding ridge fill colour, computed via blend_colors(mode = "multiply").

vline_width

A numeric value for the thickness of the vertical reference lines. Passed as linewidth to geom_vline(). Default: 0.5.

vline_alpha

A numeric value in [0, 1] for the transparency of the vertical reference lines. Default: 1.

flip

A logical value. If TRUE, the axes are swapped via coord_flip(). X-axis text angle and grid-line placement are adjusted accordingly.

alpha

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

scale

A numeric value controlling the vertical overlap of ridges. Passed to ggridges::geom_density_ridges(scale = ...). Smaller values increase overlap. When NULL, ggridges auto-computes the scale.

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.

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.

x_text_angle

A numeric value specifying the angle (in degrees) for x-axis text when flip = TRUE. Used with calc_just() to compute optimal hjust / vjust. Default: 90.

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

reverse

A logical value. If TRUE, the y-axis group order is reversed. NA groups are renamed to the literal string "NA" and placed at the end.

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_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_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_byrow

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

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.

...

Additional arguments passed to ggridges::geom_density_ridges() (bandwidth, jittered_points, quantile_lines, etc.).

Architecture

RidgePlotAtomic executes the following steps:

  1. ggplot dispatch — selects gglogger::ggplot or ggplot2::ggplot.

  2. Wide-to-long conversion — when in_form = "wide", calls tidyr::pivot_longer() on the group_by columns, producing .group (factor) and .x (values). x and group_by are redirected to these synthetic columns.

  3. Column resolution — check_columns() validates x, group_by (force_factor, allow_multi, concat_multi), and facet_by.

  4. Default group — when group_by is NULL, a synthetic .group factor with a single space character level is created so the fill pipeline runs uniformly.

  5. Reverse ordering — if reverse = TRUE, factor levels of group_by are reversed, flipping the y-axis ridge order.

  6. NA / empty handling — process_keep_na_empty() filters data. When reverse = TRUE and any group value is NA, the NA level is renamed to the literal string "NA" and moved to the end of the factor so colour mapping and display remain consistent.

  7. Palette resolution — palette_this() maps group levels to fill colours.

  8. Base ggplot — initialises ggplot(data, aes(x, y, fill)) with group_by on the y-axis.

  9. Ridge geometry — ggridges::geom_density_ridges(alpha, scale). When scale is NULL, ggridges auto-computes the overlap factor.

  10. Vertical reference lines — if add_vline is not NULL / FALSE:

    • add_vline = TRUE → computes tapply(x, group_by, mean).

    • vline_color = TRUE → resolves per-group line colours by darkening each fill colour via blend_colors(mode = "multiply"). Named list elements are matched to factor levels.

    • Adds geom_vline(xintercept, linetype, linewidth, color, alpha).

  11. Scales and labels — scale_y_discrete(drop = !keep_empty_group), scale_x_continuous(), and labs().

  12. Fill scale — scale_fill_manual(). When keep_empty_group = TRUE, drop = FALSE, breaks, and limits are set to preserve empty factor levels.

  13. Flip-aware theme — when flip = TRUE:

    • coord_flip() is applied.

    • x-axis text angle is set from x_text_angle with computed hjust / vjust via calc_just().

    • Major grid lines are drawn on the x-axis.

    • When flip = FALSE, y-axis text is right-aligned and grid lines appear on the y-axis.

  14. Theme application — do_call(theme, theme_args) applies the resolved theme function, then aspect.ratio and legend position are set.

  15. Dimension calculation — calculate_plot_dimensions(base_height = 1, n_y = nlevels(group_by), y_scale_factor = 1, aspect.ratio, legend, flip) sets height / width attributes. The base height of 1 unit per ridge keeps individual ridges compact.

  16. Faceting — facet_plot() applies facet_grid / facet_wrap, with drop = !keep_empty_facet.