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Atomic jitter plot (internal)

Source: R/jitterplot.R
JitterPlotAtomic.Rd

Core implementation for drawing a single jittered point plot. This is the workhorse behind the exported JitterPlot function — it takes a single data frame (no split_by support) and returns a ggplot object. The plot displays individual data points with random jitter along the x-axis (and optionally the y-axis) to reveal the distribution of values within each x category, making it especially useful for visualising overlapping discrete data.

The function provides extensive annotation features including point labelling (via geom_text_repel with automatic top-n selection using a configurable distance metric), point highlighting, optional dodging via group_by, and horizontal reference lines. It supports both long and wide input formats, quantile-based axis limits, and x-axis reordering by y-value summaries (mean or median).

Usage

JitterPlotAtomic(
  data,
  x,
  x_sep = "_",
  y = NULL,
  in_form = c("long", "wide"),
  keep_na = FALSE,
  keep_empty = FALSE,
  sort_x = c("none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc",
    "median"),
  flip = FALSE,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  x_text_angle = 0,
  order_by = "-({y}^2 + {size_by}^2)",
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  shape = 21,
  border = "black",
  size_by = 2,
  size_name = NULL,
  size_trans = NULL,
  y_nbreaks = 4,
  jitter_width = 0.5,
  jitter_height = 0,
  y_max = NULL,
  y_min = NULL,
  y_trans = "identity",
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_hline = NULL,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  labels = NULL,
  label_by = NULL,
  nlabel = 5,
  label_size = 3,
  label_fg = "black",
  label_bg = "white",
  label_bg_r = 0.1,
  highlight = NULL,
  highlight_color = "red2",
  highlight_size = 1,
  highlight_alpha = 1,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  ...
)

Arguments

data

A data frame.

x

A character string specifying the column name for the x-axis. Must be character or factor. Multiple columns can be provided; they are concatenated with x_sep as the separator. When in_form is "wide", the x columns are used as key columns and pivoted to long format (they are not concatenated).

x_sep

A character string used to join multiple x columns. Default "_". Ignored when x is a single column or when in_form is "wide".

y

A character string specifying the numeric column for the y-axis. Required when in_form is "long" (default). When in_form is "wide", y is not required — the values under the x columns are used as y-values.

in_form

A character string specifying the input data format. Either "long" (default) or "wide". In "long" format, x and y are separate columns. In "wide" format, the x columns contain the y-values and are pivoted to a key-value pair.

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

sort_x

A character string controlling x-axis level reordering by y-value summaries. One of "none", "mean_asc", "mean_desc", "mean", "median_asc", "median_desc", "median". "none" leaves the levels as-is. "mean_asc" / "mean" sorts by ascending mean of y. "mean_desc" sorts by descending mean. "median_asc" / "median" sorts by ascending median. "median_desc" sorts by descending median. Default: "none".

flip

A logical value. When TRUE, the x and y axes are swapped via coord_flip and the x-axis factor levels are reversed. Dimension calculation accounts for the flip. Default: FALSE.

group_by

A character vector of column names for dodging the points. Each unique combination becomes a separate dodge group and the points are offset horizontally via position_jitterdodge to reduce overlap. Multiple columns are concatenated with group_by_sep. When NULL (default), no dodging is applied — only jitter via position_jitter.

group_by_sep

A character string used to join multiple group_by columns. Default "_".

group_name

A character string for the dodge-group legend title. When NULL (default), the group_by column name is used.

x_text_angle

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

order_by

A string expression passed to arrange() to determine which points are labelled. Evaluated within each x-group (and facet panel when facet_by is set). Default: "-({y}^2 + {size_by}^2)", which selects points farthest from the origin in y-size radial distance, analogous to VolcanoPlot.

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 in [0, 1] controlling point transparency. Default: 1.

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.

shape

A numeric value specifying the point shape (ggplot2 point shape codes). Shapes 21–25 are filled shapes with borders; for these shapes the border behaviour is controlled by border. Default: 21 (filled circle).

border

Controls the border of points when the shape has a border (21–25). If TRUE, the border colour follows the point fill colour (same as the group colour). If a single colour string (e.g. "black"), uses that constant border colour for all points. If FALSE, no border is drawn (NA). Default: "black".

size_by

A numeric column name or a single numeric value controlling point size. When a column name is provided, sizes are scaled using scale_size_area(max_size = 6) and a size legend is shown. When a single numeric value, all points use that constant size. Default: 2.

size_name

A character string for the size legend title. When NULL (default) and size_by is a column, the column name is used. Ignored when size_by is a single numeric value.

size_trans

A function or a function name (as a string) to transform the size_by values for size mapping. The transformed values determine the point size on the plot, but the legend labels show the original (untransformed) values. When NULL (default), no transformation is applied.

y_nbreaks

A numeric value hinting at the number of break intervals for the y-axis. Passed to scale_y_continuous. Default: 4.

jitter_width

A numeric value controlling the amount of horizontal jitter (in x-axis units). Passed to position_jitter / position_jitterdodge. Default: 0.5.

jitter_height

A numeric value controlling the amount of vertical jitter (in y-axis units). Passed to position_jitter / position_jitterdodge. Default: 0.

y_max, y_min

Numeric values or quantile strings (e.g. "q95", "q5") for y-axis limits used in coord_cartesian / coord_flip. When NULL (default), the data range is used. When a quantile string, the corresponding quantile of the y-values is computed via quantile().

y_trans

A character string specifying a transformation for the y-axis (e.g. "log10", "sqrt"). Passed to scale_y_continuous. Default: "identity".

add_bg

A logical value. When TRUE, alternating background stripes are drawn behind the points via bg_layer(), using the x-axis level order. Default: FALSE.

bg_palette

A character string specifying the palette for the background stripe colours. Passed to bg_layer(). Default: "stripe".

bg_palcolor

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

bg_alpha

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

add_hline

One or more numeric values specifying y-values at which to draw horizontal reference lines. When NULL (default), no reference lines are drawn.

hline_type

A character string specifying the line type for the horizontal reference line(s). Default: "solid".

hline_width

A numeric value specifying the line width for the horizontal reference line(s). Default: 0.5.

hline_color

A character string specifying the colour for the horizontal reference line(s). Default: "black".

hline_alpha

A numeric value in [0, 1] specifying the alpha (transparency) for the horizontal reference line(s). Default: 1.

labels

A vector of row names or row indices specifying which points to label. When NULL (default) and nlabel > 0, the top nlabel points per x-group are selected automatically.

label_by

A character string naming a column whose values are used as label text. When NULL (default), row names are used as labels.

nlabel

An integer specifying the number of points to label per x-group when labels is NULL. Points are selected by descending order of order_by. Default: 5. Set to 0 to suppress automatic labelling.

label_size, label_fg, label_bg, label_bg_r

Label aesthetics for geom_text_repel. label_size: text size (default 3). label_fg: text colour (default "black"). label_bg: background (halo) colour for the label text (default "white"). label_bg_r: background border radius (default 0.1).

highlight

A specification of which points to highlight. Can be: TRUE (highlight all points), a numeric vector of row indices, a single character string parsed as an R expression, or a character vector of row names. When a point is highlighted, an overlay geom_point is drawn on top with highlight_color, highlight_size, and highlight_alpha. Default: NULL (no highlighting).

highlight_color

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

highlight_size

A numeric value specifying the size of highlighted points. Default: 1.

highlight_alpha

A numeric value in [0, 1] specifying the transparency of highlighted points. Default: 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_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.

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.

seed

The random seed to use. Default is 8525.

...

Additional arguments.

Value

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

Architecture

  1. ggplot dispatch — selects gglogger::ggplot or ggplot2::ggplot based on getOption("plotthis.gglogger.enabled").

  2. in_form handling — when in_form = "wide", the x columns are pivoted to long format via pivot_longer(), creating a key column .x and a value column .y.

  3. Column resolution — x, y, group_by, and facet_by are validated and transformed via check_columns. Multi-column inputs for x and group_by are concatenated into single columns using their respective separators (x_sep, group_by_sep).

  4. NA / empty-level handling — process_keep_na_empty() applies keep_na and keep_empty policies. Per-column keep_empty settings are extracted for x, group_by, and facet_by independently. When facet_by has more than one column, the keep_empty values for all facet columns must be identical.

  5. sort_x resolution — match.arg() normalises the sort_x argument, and per-group (x, group_by, facet_by) means and medians of y are computed for subsequent reordering.

  6. y-axis limit computation — y_max and y_min support raw numeric values or quantile strings (e.g. "q95"), which are resolved via quantile(). These limits are used for fixed coord_cartesian / coord_flip.

  7. Highlight flag — when highlight is provided, a logical column .highlight is created. Values can be TRUE (all points), a numeric vector of row indices, a single character string parsed as an R expression, or a character vector matched against row names.

  8. Label preparation — labels are resolved from label_by or row names. When labels is NULL and nlabel > 0, the top nlabel points per x-group are selected by descending order of order_by (default: -({y}^2 + {size_by}^2), the radial distance from zero in y-size space, analogous to VolcanoPlot). When facet_by is active, the ranking is nested within each facet panel.

  9. x-axis reordering — when sort_x is not "none", the x-axis factor levels are reordered by the per-group mean or median via reorder().

  10. Flip handling — when flip = TRUE, the x-axis factor levels are reversed and the aspect ratio is inverted.

  11. Colour assignment — palette_this() assigns colours to the levels of group_by (or x when group_by is NULL), including NA levels which are relabelled as "NA".

  12. Background layer — when add_bg = TRUE, alternating background stripes are drawn via bg_layer() using the x-axis level order.

  13. Position jitter — when group_by is NULL, position_jitter() is used. When group_by is provided, position_jitterdodge() is used so points are dodged by group before jittering.

  14. Pre-compute jittered positions — a temporary ggplot is built and rendered via ggplot_build() to extract the actual jittered coordinates. These are stored as .x_jittered and .y_jittered columns and used by the label layer because geom_text_repel does not natively respect position_jitter / position_jitterdodge.

  15. Point layer — geom_point() is built with the appropriate aesthetic mapping: fill (for shapes 21–25) or colour (for other shapes) mapped to the grouping variable. Border behaviour for shapes 21–25 is controlled by border (constant string, mapped to group colour, or NA). When size_by is a column, size is mapped via aes(size).

  16. Discrete colour/fill scales — scale_fill_manual() or scale_color_manual() with the assigned palette colours. When keep_empty is TRUE for the colour column, drop = FALSE and explicit breaks / limits preserve empty levels. An additional scale_color_manual() is added for border colour when border = TRUE.

  17. Size scale — when size_by is a column, scale_size_area(max_size = 6) is applied. If size_trans is provided, the legend labels show the original (untransformed) values while the mapping uses transformed values.

  18. Highlight overlay — if any points are highlighted, a second geom_point() layer is drawn on top using the highlight_color, highlight_size, and highlight_alpha settings. The highlight layer does not affect the legend.

  19. Label layer — if any points are selected for labelling, geom_text_repel() is rendered at the pre-computed jittered coordinates.

  20. Horizontal reference lines — when add_hline is provided, geom_hline() is drawn using the specified line aesthetics.

  21. Axes and labels — scale_x_discrete() (with drop = !isTRUE(keep_empty_x)), scale_y_continuous(trans = y_trans, n.breaks = y_nbreaks), and labs() set the axis scale properties and titles.

  22. Coordinate system — when flip = TRUE, coord_flip() is used with (or without) fixed y-limits depending on free-scale faceting. When flip = FALSE, coord_cartesian() sets the y-axis limits unless free scales are in use.

  23. Theme — do_call(theme, theme_args) applies the selected theme, with additional aspect.ratio, x-axis text rotation, legend position, and legend direction adjustments. Panel grid lines are styled: major y-axis lines (dashed grey) for non-flipped plots; major x-axis lines for flipped plots.

  24. Dimension calculation — calculate_plot_dimensions() computes plot height and width from the x-axis category count, aspect.ratio, dodge group count, legend metrics, and label character width. The minimum dimensions account for x-axis label length. The resulting height / width attributes are stored on the ggplot object. For flipped plots, the width is set to at least max(width, height).

  25. Faceting — facet_plot() wraps the plot with facet_wrap / facet_grid if facet_by is provided, respecting the keep_empty setting for facet variables.