UpsetPlotAtomic: Atomic UpSet plot (internal)

In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

Atomic UpSet plot (internal)

Description

Core implementation for drawing a single UpSet plot. This is the internal workhorse behind the exported UpsetPlot function — it takes a single data partition (no split_by support) and returns a ggplot object. The plot comprises three visual components:

• A horizontal bar chart (top) showing the size of each intersection, with bars filled by a gradient of intersection count.

• A set-size bar chart (left) showing the total number of elements in each set (added automatically by ggupset).

• A combination matrix (bottom) where rows are sets, columns are intersections, and dots indicate set membership. Connected dots trace the intersection pattern.

Usage

UpsetPlotAtomic(
  data,
  in_form = "auto",
  group_by = NULL,
  group_by_sep = "_",
  id_by = NULL,
  label = TRUE,
  label_fg = "black",
  label_size = NULL,
  label_bg = "white",
  label_bg_r = 0.1,
  palette = "material-indigo",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  specific = TRUE,
  combmatrix_gap = 6,
  theme = "theme_this",
  theme_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  aspect.ratio = 0.6,
  legend.position = "right",
  legend.direction = "vertical",
  levels = NULL,
  ...
)

Arguments

data	A data frame.
in_form	A character string specifying the input format. One of "auto" (default; detect from data structure), "long", "wide", "list", or "upset".
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
id_by	A character string specifying the column name for instance identifiers. Required for long format; optional for wide format (a synthetic .id column is created if omitted).
label	A logical value. When TRUE (default), count labels are displayed above each intersection bar via geom_text_repel().
label_fg	A character string specifying the colour of the label text. Default: "black".
label_size	A numeric value specifying the size of the label text. Default: NULL (computed from base_size / 12 * 3.5).
label_bg	A character string specifying the background fill colour of the label. Default: "white".
label_bg_r	A numeric value specifying the corner radius of the label background, passed to geom_text_repel(bg.r). Default: 0.1.
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.
specific	A logical value. When TRUE (default), only specific intersections are returned (elements belonging exclusively to the shown set combination). When FALSE, all overlapping items are included. See https://github.com/gaospecial/ggVennDiagram/issues/64.
combmatrix_gap	A numeric value specifying the gap between rows of the combination matrix, measured at base_size = 12. The actual gap is scaled by text_size_scale = base_size / 12. Default: 6.
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.
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.
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.
levels	A character vector of set levels to include, in display order. When NULL (default), all detected sets are shown. Accepted for compatibility but not currently used by the internal implementation.
...	Additional arguments passed to scale_x_upset. Useful options include n_sets and n_intersections to limit the number of shown sets / intersections.

Value

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

Architecture

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

2. Data preparation — prepare_upset_data() converts the input into the internal UpsetPlotData format with an Intersection list-column (set-membership labels per element) and a "group_order" attribute for set ordering.

3. Text scale — base_size from theme_args (default 12) drives a text_size_scale that proportionally scales the combination-matrix row gap, label sizes, and point sizes.

4. Bar geom — geom_bar() counts rows per intersection. Bars are filled by count via scale_fill_gradientn() with colours from palette_this().

5. Bar labels — when label = TRUE, geom_text_repel() places count labels above each bar, with configurable foreground, background, and size.

6. Scale x upset — ggupset::scale_x_upset(...) is called, returning two components: a ScaleUpset (index [[1]]) and a CoordCombMatrix (index [[2]]). Only the scale is applied; the bundled coord is discarded to avoid a "Coordinate system already present" conflict.

7. Labels and theme — labs() sets title, subtitle, and axis text. do_call(theme, theme_args) applies the chosen theme. Aspect ratio, legend position, legend direction, and grid lines are configured.

8. Combination matrix — ggupset::axis_combmatrix() builds the lower panel via an override_plotting_function:

   • Reorders rows to match group_order (reversed for top-to-bottom set listing).

   • Alternating row backgrounds via geom_rect() with white / #F7F7F7 fills.

   • Set-membership dots (geom_point()) in black for present and #E0E0E0 for absent.

   • Connecting lines (geom_line()) through observed dots to trace the intersection pattern.

9. Matrix theme — ggupset::theme_combmatrix() applies the combination-matrix appearance with combmatrix_gap between rows (scaled by text_size_scale).

10. Dimension calculation — calculate_plot_dimensions() computes height from n_sets and width from n_intersections, both passed via ... (default 99). aspect.ratio is used as a standard H/W coupling with x_scale_factor = 0.6. An additional width adjustment accounts for set-label character width.

plotthis documentation built on July 9, 2026, 5:07 p.m.