QQPlotAtomic: Atomic QQ/PP plot
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

QQPlotAtomic

R Documentation

Atomic QQ/PP plot

Description

Core implementation for drawing a single quantile-quantile (QQ) or probability-probability (PP) plot. This is the internal workhorse dispatched by the exported QQPlot function – it takes a single data frame (no split_by support) and returns a ggplot object. The function compares the empirical distribution of a numeric variable against a theoretical distribution (default: standard normal) via the qqplotr package.

Two plot types are supported via the type parameter:

QQ plot (type = "qq", the default) – plots sample quantiles against theoretical quantiles. Deviations from the reference line indicate departures from the assumed distribution (skewness, heavy tails, outliers).
PP plot (type = "pp") – plots empirical cumulative probability against theoretical cumulative probability. PP plots are more sensitive to deviations in the centre of the distribution, while QQ plots are more sensitive at the tails.

The function can overlay confidence bands (band) around the reference line using several methods (pointwise confidence intervals, Kolmogorov-Smirnov, Tukey's simultaneous intervals, or bootstrap). Multiple bands can be combined and each receives a separate fill colour from the palette.

Usage

QQPlotAtomic(
  data,
  val,
  val_trans = NULL,
  type = c("qq", "pp"),
  band = NULL,
  line = list(),
  point = list(),
  fill_name = "Bands",
  band_alpha = 0.5,
  theme = "theme_this",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  palreverse = FALSE,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = waiver(),
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  seed = 8525,
  xlim = NULL,
  ylim = NULL,
  xlab = ifelse(type == "qq", "Theoretical Quantiles", "Probability Points"),
  ylab = ifelse(type == "qq", "Sample Quantiles", "Cumulative Probability"),
  ...
)

Arguments

`data`	A data frame.
`val`	A character string naming the numeric column whose distribution is compared against the theoretical distribution.
`val_trans`	A transformation function applied to the `val` column before plotting. For example, `log` or `sqrt`. Default: `NULL` (no transformation).
`type`	A character string specifying the plot type. Either `"qq"` (quantile-quantile, the default) or `"pp"` (probability-probability). Partial matching is supported.
`band`	A list of arguments passed to `stat_qq_band` or `stat_pp_band`, depending on `type`. Set to `TRUE` or an empty list to use default arguments. Set to `NULL` (the default) to suppress bands entirely. To add multiple bands, provide a list of lists, each containing arguments for one band (e.g. different `bandType` or `distribution`). Each band can also include a custom `mapping` aesthetic to control its fill colour legend entry.
`line`	A list of arguments passed to `stat_qq_line` or `stat_pp_line`, depending on `type`. Default: `list()` (adds a reference line with default arguments). Set to `NULL` to omit the line entirely.
`point`	A list of arguments passed to `stat_qq_point` or `stat_pp_point`, depending on `type`. Default: `list()` (adds points with default arguments). Set to `NULL` to omit points (not recommended).
`fill_name`	A character string for the fill legend title used when bands are present. Default: `"Bands"`.
`band_alpha`	A numeric value in `[0, 1]` setting the transparency of all bands. Individual bands can override this via `alpha` inside the `band` argument list. Default: `0.5`.
`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.
`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.
`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.
`seed`	A numeric value for the random seed used internally. Default: `8525`. Passed to `set.seed`.
`xlim`	A numeric vector of length 2 specifying the x-axis limits. Default: `NULL` (use data range).
`ylim`	A numeric vector of length 2 specifying the y-axis limits. Default: `NULL` (use data range).
`xlab`	A character string specifying the x-axis label.
`ylab`	A character string specifying the y-axis label.
`...`	Additional arguments.

Value

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

Architecture

QQPlotAtomic executes the following steps:

ggplot dispatch – selects gglogger::ggplot or ggplot2::ggplot based on getOption("plotthis.gglogger.enabled").
Type validation – match.arg() resolves type to "qq" or "pp".
Input validation – stopifnot() checks that band is TRUE, a list, or NULL; line and point are lists or NULL; and xlim/ylim are numeric vectors of length 2 or NULL.
Column resolution – check_columns() validates the val column.
Value transformation – when val_trans is provided, it is applied to the val column (e.g. log-transform).
Base ggplot – initialises ggplot(data, aes(sample = !!sym(val))). The sample aesthetic is the standard interface for qqplotr.
Band rendering – when band is not NULL:
1. Selects the band stat function: qqplotr::stat_qq_band for QQ plots or qqplotr::stat_pp_band for PP plots.
2. Converts band = TRUE to an empty list (default arguments).
3. Normalises a single band (non-list or named list) into a list-of-lists format.
4. Iterates over bands, assigning each a default fill aesthetic ("Band_1", "Band_2", ..., up to a maximum of 10). The user can override the fill mapping via mapping inside each band's argument list.
5. Sets alpha per band, falling back to the band_alpha parameter.
6. Adds each band to the plot via do_call(band_fn, bnd).
Legend position resolution – if no bands were rendered or all bands use default "Band_" names, the legend defaults to "none" (when legend.position is a waiver); otherwise defaults to "right".
Reference line – when line is not NULL, adds qqplotr::stat_qq_line (QQ) or qqplotr::stat_pp_line (PP) via do_call().
Points – when point is not NULL, adds qqplotr::stat_qq_point (QQ) or qqplotr::stat_pp_point (PP) via do_call().
Fill colour scale – when bands are present, scale_fill_manual() is added with colours resolved via palette_this() using the band names, palette, palcolor, and palreverse. The legend title is set to fill_name.
Axis limits – ggplot2::xlim() and ggplot2::ylim() are applied if xlim or ylim are set.
Labels and theme – labs(title, subtitle, x, y) with fallback to val for axis labels; do_call(theme, theme_args); ggplot2::theme() with aspect.ratio, panel.grid.major (grey80, dashed), legend.position, and legend.direction.
Dimension calculation – calculate_plot_dimensions() with base_height = 4.5, aspect.ratio, and legend metrics (number of bands, band name character width).
Faceting – facet_plot() applies facet_wrap / facet_grid if facet_by is provided.