Package 'eulerr'

Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.
Authors: Johan Larsson [aut, cre] (ORCID: <https://orcid.org/0000-0002-4029-5945>), A. Jonathan R. Godfrey [ctb], Peter Gustafsson [ctb], David H. Eberly [ctb] (geometric algorithms), Emanuel Huber [ctb] (root solver code), Florian Privé [ctb]
Maintainer: Johan Larsson <[email protected]>
License: GPL-3
Version: 8.0.0.9000
Built: 2026-06-03 21:56:54 UTC
Source: https://github.com/jolars/eulerr

Help Index

Error plot for euler objects

Description

This is a diagnostic tool for evaluating the fit from a call to euler() visually. A color key is provided by default, which represents the chosen error metric so that one can easily detect which areas in the diagram to be skeptical about.

Usage

error_plot(
  x,
  type = c("regionError", "residuals"),
  quantities = TRUE,
  pal = NULL,
  ...
)

Arguments

x

an object of class euler, typically the result of a call to euler().
type

error metric. 'regionError' is the difference in percentage points from the input
quantities

whether to draw the error metric on the plot
pal

color palette for the fills in the legend
...

arguments passed down to plot.euler(). Currently, providing fills, legend, or strips are not allowed and will return a warning.

Details

Notice that this function is purely provided for diagnostic reasons and does not come with the same kind of customization that plot.euler() provides: the color legend can only be customized in regards to its color palette and another key (instead of labels) is completely turned off.

Value

Returns an object of class eulergram, which will be plotted on the device in the same manner as objects from plot.euler(). See plot.eulergram() for details.

See Also

plot.euler(), euler(), plot.eulergram()

Examples

error_plot(euler(organisms), quantities = FALSE)

Area-proportional Euler diagrams

Description

Fit Euler diagrams (a generalization of Venn diagrams) using numerical optimization to find exact or approximate solutions to a specification of set relationships. The shape of the diagram may be a circle, an ellipse, an axis-aligned rectangle, or an axis-aligned square.

Usage

euler(combinations, ...)

## Default S3 method:
euler(
  combinations,
  input = c("disjoint", "union"),
  transform = identity,
  shape = c("circle", "ellipse", "rectangle", "square"),
  loss = c("sum_squared", "sum_absolute", "sum_absolute_region_error",
    "sum_squared_region_error", "max_absolute", "max_squared", "root_mean_squared",
    "stress", "diag_error"),
  loss_aggregator = NULL,
  complement = NULL,
  control = list(),
  ...
)

## S3 method for class 'data.frame'
euler(
  combinations,
  weights = NULL,
  by = NULL,
  sep = "_",
  factor_names = TRUE,
  ...
)

## S3 method for class 'matrix'
euler(combinations, ...)

## S3 method for class 'table'
euler(combinations, ...)

## S3 method for class 'list'
euler(combinations, ...)

Arguments

combinations

set relationships as a named numeric vector, matrix, or data.frame (see methods (by class))
...

arguments passed down to other methods
input

type of input: disjoint identities ('disjoint') or unions ('union').
transform

a function applied to the areas of the disjoint (exclusive) regions before fitting. The default, base::identity(), leaves the areas untouched. A monotone transform such as base::log1p() can keep small regions legible when set sizes span several orders of magnitude. The transform is applied to the exclusive regions because those are the additive atoms the diagram fits to; as a consequence the area of a whole set or union no longer equals transform() of its size, only the individual visible regions carry the transformed scale. The function must return a non-negative, finite value for each region (and for complement, when given). Has no effect on venn() diagrams, whose geometry is fixed.
shape

geometric shape used in the diagram
loss

type of loss to minimize over. The default, "sum_squared", minimizes the sum of squared errors. The available options mirror the loss functions exposed by the eunoia Rust crate that powers the optimizer:

  • "sum_squared" — normalized sum of squared errors (default).

  • "sum_absolute" — normalized sum of absolute errors.

  • "sum_absolute_region_error" — normalized sum of absolute region errors.

  • "sum_squared_region_error" — normalized sum of squared region errors.

  • "max_absolute" — normalized maximum absolute error.

  • "max_squared" — normalized maximum squared error.

  • "root_mean_squared" — normalized root-mean-squared error.

  • "stress" — venneuler-style stress.

  • "diag_error" — eulerAPE-style diagError.

loss_aggregator

deprecated; use loss directly instead. Pre-1.0 code that combined loss ("square"/"abs"/"region") with loss_aggregator ("sum"/"max") still works but emits a warning; the combination is mapped to the equivalent new loss value.
complement

an optional single non-negative number giving the area of the complement — that is, the universe outside every named set. When supplied, the fitter jointly optimizes a containing rectangle together with the diagram shapes so that the area of the rectangle minus the union of (clipped) shapes matches complement. This is the classical "everything not in any set" region; see plot.euler() for how it is rendered. Defaults to NULL (no container; classical shape-only fit). Not supported for venn().
control

a list of control parameters.

  • extraopt: should the global-search fallback optimizer (CMA-ES) kick in when the primary optimizer's diagError exceeds extraopt_threshold? The default is TRUE for three-set ellipse fits and FALSE otherwise.

  • extraopt_threshold: threshold, in terms of diagError, for when the CMA-ES fallback kicks in. A value of 0 means it will kick in for any error; a value of 1 means it will never kick in. Default 0.001.

  • tolerance: convergence tolerance passed to the underlying solver. Tighter values give more accurate fits at higher cost. Default 1e-8.

  • max_sets: maximum number of sets the underlying engine will accept. Defaults to NULL, which uses the engine's built-in default of 32. Region masks are stored in a bitset, so values may be raised up to 63 (the absolute hard cap). Going higher is rarely useful in practice since fully-overlapping diagrams have 2^n - 1 regions.

weights

a numeric vector of weights of the same length as the number of rows in combinations.
by

a factor or character matrix to be used in base::by() to split the data.frame or matrix of set combinations
sep

a character to use to separate the dummy-coded factors if there are factor or character vectors in 'combinations'.
factor_names

whether to include factor names when constructing dummy codes

Details

If the input is a matrix or data frame and argument by is specified, the function returns a list of euler diagrams.

The function minimizes the residual sums of squares,

∑i=1n(Ai−ωi)2,\sum_{i=1}^n (A_i - \omega_i)^2,

by default, where ωi\omega_i the size of the ith disjoint subset, and AiA_i the corresponding area in the diagram, that is, the unique contribution to the total area from this overlap. The loss function can, however, be controlled via the loss argument.

euler() also returns stress (from venneuler), as well as diagError, and regionError from eulerAPE.

The stress statistic is computed as

∑i=1n(Ai−βωi)2∑i=1nAi2,\frac{\sum_{i=1}^n (A_i - \beta\omega_i)^2}{\sum_{i=1}^n A_i^2},

where

β=∑i=1nAiωi/∑i=1nωi2.\beta = \sum_{i=1}^n A_i\omega_i / \sum_{i=1}^n \omega_i^2.

regionError is computed as

∣Ai∑i=1nAi−ωi∑i=1nωi∣.\left| \frac{A_i}{\sum_{i=1}^n A_i} - \frac{\omega_i}{\sum_{i=1}^n \omega_i}\right|.

diagError is simply the maximum of regionError.

Value

A list object of class 'euler' with the following parameters.

shapes

a data frame of fitted shape parameters. One row per set with a type column (one of "circle", "ellipse", "rectangle", "square"), the center coordinates h and k, and the shape-specific columns: a, b, phi for ellipses/circles; width and height for rectangles; side (plus mirrored width/height) for squares. Columns that don't apply to the chosen shape are NA.
ellipses

for shape = "circle" and shape = "ellipse" fits, the legacy 5-column data frame of h, k, a, b, phi. This slot is deprecated in favour of shapes and is not populated for rectangle/square fits.
original.values

set relationships in the input
fitted.values

set relationships in the solution
residuals

residuals
regionError

the difference in percentage points between each disjoint subset in the input and the respective area in the output
diagError

the largest regionError
stress

normalized residual sums of squares

Methods (by class)

  • euler(default): a named numeric vector, with combinations separated by an ampersand, for instance A&B = 10. Missing combinations are treated as being 0.

  • euler(data.frame): a data.frame of logicals, binary integers, or factors.

  • euler(matrix): a matrix that can be converted to a data.frame of logicals (as in the description above) via base::as.data.frame.matrix().

  • euler(table): A table with max(dim(x)) < 3.

  • euler(list): a list of vectors, each vector giving the contents of that set (with no duplicates). Vectors in the list must be named.

References

Wilkinson L. Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams. IEEE Transactions on Visualization and Computer Graphics (Internet). 2012 Feb (cited 2016 Apr 9);18(2):321-31. Available from: doi:10.1109/TVCG.2011.56

Micallef L, Rodgers P. eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses. PLOS ONE (Internet). 2014 Jul (cited 2016 Dec 10);9(7):e101717. Available from: doi:10.1371/journal.pone.0101717

See Also

plot.euler(), print.euler(), eulerr_options(), venn()

Examples

# Fit a diagram with circles
combo <- c(A = 2, B = 2, C = 2, "A&B" = 1, "A&C" = 1, "B&C" = 1)
fit1 <- euler(combo)

# Investigate the fit
fit1

# Refit using ellipses instead
fit2 <- euler(combo, shape = "ellipse")

# Investigate the fit again (which is now exact)
fit2

# Plot it
plot(fit2)

# A set with no perfect solution
euler(c(
  "a" = 3491, "b" = 3409, "c" = 3503,
  "a&b" = 120, "a&c" = 114, "b&c" = 132,
  "a&b&c" = 50
))


# Using grouping via the 'by' argument through the data.frame method
euler(fruits, by = list(sex, age))


# Using the matrix method
euler(organisms)

# Using weights
euler(organisms, weights = c(10, 20, 5, 4, 8, 9, 2))

# The table method
euler(pain, factor_names = FALSE)

# A euler diagram from a list of sample spaces (the list method)
euler(plants[c("erigenia", "solanum", "cynodon")])

Compose Euler Diagrams

Description

Arrange two eulergram objects side-by-side or stacked, building up multi-panel layouts with operator syntax. Compositions can be nested arbitrarily, e.g. (p1 | p2) / p3.

Usage

## S3 method for class 'eulergram'
e1 | e2

## S3 method for class 'eulergram'
e1 / e2

Arguments

e1, e2

eulergram objects, typically returned by plot.euler().

Details

| arranges the two plots horizontally; / stacks them vertically. The result is itself an eulergram, so further composition chains naturally.

The gap between adjacent plots is controlled by the composition$spacing entry of eulerr_options(), which must be a grid::unit() and defaults to grid::unit(1, "lines").

Because composition is binary and recursive, panels at different nesting levels are not size-aligned. In (p1 | p2) / p3, p3 spans the full bottom row while p1 and p2 split the top row equally.

Value

An eulergram containing the composed layout.

See Also

plot.euler(), eulerr_options()

Examples

p1 <- plot(euler(c(A = 1, B = 8, "A&B" = 1)))
p2 <- plot(euler(c(A = 1, C = 1, "A&C" = 1)))

p1 | p2
p1 / p2

p3 <- plot(euler(c(X = 3, Y = 2, "X&Y" = 1)))
(p1 | p2) / p3

Get or set global graphical parameters for eulerr

Description

This function provides a means to set default parameters for functions in eulerr. Query eulerr_options() (without any argument) to see all the available options and read more about the plot-related ones in grid::gpar() and graphics::par().

Usage

eulerr_options(...)

Arguments

...

objects to update the global graphical parameters for eulerr with.

Details

Currently, the following items will be considered:

pointsize

size in pts to be used as basis for fontsizes and some margin sizes in the resulting plot

#'

fills

a list of items fill and alpha

patterns

a list of items type, angle, col, lwd, and alpha

edges

a list of items col, alpha, lex, lwd, and lty

labels

a list of items rot, col, alpha, fontsize, cex, fontfamily, fontface, lineheight, and font

quantities

a list of items type, template, format, total, rot, col, alpha, fontsize, cex, fontfamily, lineheight, and font

annotations

a list of items rot, col, alpha, fontsize, cex, fontfamily, lineheight, font, and labels (a named character vector keyed by subset name). Used to add a third stacked text element per region below the quantity.

strips

col, alpha, fontsize, cex, fontfamily, lineheight, and font

legend

arguments to grid::legendGrob() as well as col, alpha, fontsize, cex, symbol_size (symbol size multiplier, independent of text size; defaults to cex if NULL), fontfamily, lineheight, and font

main

arguments to grid::textGrob()

complement

a list of styling defaults for the container box and its complement label drawn when euler() is called with ⁠complement =⁠. Items: fill, alpha, col, lty, lwd, lex, fontsize, cex, font, fontfamily, lineheight. The default lty = 2 draws the container with a dashed outline.

padding

a grid::unit() giving the padding between various elements in plots from plot.euler(), which you can change if you, for instance, want to increase spacing between labels, quantities, and percentages.

composition

a list controlling how eulergram objects are arranged when composed via | or /. Contains a single spacing item (a grid::unit()) that sets the gap between adjacent plots.

Value

This function gets or sets updates in the global environment that are used in plot.euler().

See Also

plot.euler(), grid::gpar(), graphics::par()

Examples

eulerr_options(edges = list(col = "blue"), fontsize = 10)
eulerr_options(n_threads = 2)

Fitted values of euler object

Description

Fitted values of euler object

Usage

## S3 method for class 'euler'
fitted(object, dense = FALSE, ...)

Arguments

object

object of class 'euler'
dense

if TRUE, return a vector covering every combination of the non-empty sets (2^n - 1 entries), filling absent combinations with 0. The default (FALSE) returns the sparse vector stored on the object, which only contains entries that were either requested as input or fit to a non-zero area. Use dense = TRUE only for diagrams with few sets — the full enumeration is exponential in the number of non-empty sets.
...

ignored

Value

A named numeric vector of fitted areas keyed by combination label (set names joined by &).

Fruits

Description

A synthethic data set of preferences for fruits and their overlaps, generated only to be a showcase for the examples for this package.

Usage

fruits

Format

A data.frame with 100 observations of 5 variables:

banana

whether the person likes bananas, a logical

apple

whether the person likes apples, a logical

orange

whether the person likes oranges, a logical

sex

the sex of the person, a factor with levels 'male' and 'female'

age

the age of the person, a factor with levels 'child' and 'adult'

Organisms

Description

Example data from the VennMaster package.

Usage

organisms

Format

A matrix with 7 observations, consisting of various organisms, and 5 variables: animal, mammal, plant, sea, and, spiny, indicating whether the organism belongs to the category or not.

Details

Note that this data is difficult to fit using an Euler diagram, even if we use ellipses, which is clear if one chooses to study the various overlaps in the resulting diagrams.

Source

https://github.com/sysbio-bioinf/VennMaster/blob/master/data_examples/deploy/example1.list

Pain distribution data

Description

Data from a study on pain distribution for patients with persistent neck pain in relation to a whiplash trauma.

Usage

pain

Format

A flat table (cross-table) with with sex in columns and pain distribution in rows and integer counts making up the cells of the table.

Disclaimer

Note that the maintainer of this package is an author of the source for this data.

Source

Westergren H, Larsson J, Freeman M, Carlsson A, Jöud A, Malmström E-M. Sex-based differences in pain distribution in a cohort of patients with persistent post-traumatic neck pain. Disability and Rehabilitation. 2017 Jan 27

Plants

Description

Data on plants and the states in the US and Canada they occur in.

Usage

plants

Format

A list with 33,721 plants, each containing a character vector listing the states in the US and Canada in which they occur. The names in the list specify the species or genus of the plant.

Source

USDA, NRCS. 2008. The PLANTS Database, 31 December 2008). National Plant Data Center, Baton Rouge, LA 70874-4490 USA.

Dua, D. and Karra Taniskidou, E. (2017). UCI Machine Learning Repository http://archive.ics.uci.edu/ml/. Irvine, CA: University of California, School of Information and Computer Science.

Plot Euler and Venn diagrams

Description

Plot diagrams fit with euler() and venn() using grid::Grid() graphics. This function sets up all the necessary plot parameters and computes the geometry of the diagram. plot.eulergram(), meanwhile, does the actual plotting of the diagram. Please see the Details section to learn about the individual settings for each argument.

Usage

## S3 method for class 'euler'
plot(
  x,
  fills = TRUE,
  patterns = FALSE,
  edges = TRUE,
  legend = FALSE,
  labels = identical(legend, FALSE),
  quantities = FALSE,
  annotations = NULL,
  strips = NULL,
  bg = FALSE,
  main = NULL,
  complement = TRUE,
  rotate = 0,
  n = 200L,
  adjust_labels = TRUE,
  ...
)

## S3 method for class 'eulerr_venn'
plot(
  x,
  fills = TRUE,
  patterns = FALSE,
  edges = TRUE,
  legend = FALSE,
  labels = identical(legend, FALSE),
  quantities = TRUE,
  strips = NULL,
  bg = FALSE,
  main = NULL,
  complement = TRUE,
  n = 200L,
  adjust_labels = TRUE,
  ...
)

## S3 method for class 'venn'
plot(...)

Arguments

x

an object of class 'euler', generated from euler()
fills

a logical, vector, or list of graphical parameters for the fills in the diagram. Vectors are assumed to be colors for the fills. See grid::grid.path(). Named fill vectors can be matched in fills$mode = "disjoint" (default) or fills$mode = "union".
patterns

a logical, vector, or list of graphical parameters for fill patterns in the diagram. Vectors are assumed to be pattern types (currently "stripes" or NA), where NA means no pattern. Supported list items are type, angle, col, lwd, and alpha. Named pattern vectors can be matched in patterns$mode = "disjoint" (default) or patterns$mode = "union".
edges

a logical, vector, or list of graphical parameters for the edges in the diagram. Vectors are assumed to be colors for the edges. See grid::grid.polyline().
legend

a logical scalar or list. If a list, the item side can be used to set the location of the legend and symbol_size can be used to scale the legend symbols independently of the text size. See grid::grid.legend().
labels

a logical, vector, or list. Vectors are assumed to be text for the labels. See grid::grid.text(). In addition to the grid::gpar() fields, the following placement controls are supported (delegated to the eunoia Rust crate): labels$placement ("raycast" (default), "force_directed", or "elbow") selects the strategy used when a label does not fit inside its region. "raycast" and "force_directed" produce straight leader lines (the former places the label along the centroid→POI ray, the latter relaxes labels with a polygon-aware force solver). "elbow" produces d3-pie style orthogonal leaders, stacking exterior labels in left/right columns reached by a three-segment polyline. labels$margin (numeric) overrides the per-region margin between an exterior label and the diagram (default is half the larger of the label's width and height); labels$tether ("poi" (default) or "boundary") chooses where the leader line attaches on the source region; labels$gap controls the visible gap between the leader tip and the label box edge — a bare numeric is interpreted as lines (font-relative), a grid::unit() is honored as given, and the default NULL tracks eulerr_options()$padding so the gap matches the spacing between label and quantity; labels$leader is a list (col, alpha, lwd, lty, lex) styling the leader line drawn from the tether to the exterior label. Strategy-specific knobs live in their own sublists: labels$force_directed = list(iterations = ...) sets the iteration cap for the force-directed solver, and labels$elbow = list(min_gap = ...) sets the minimum vertical centre-to-centre spacing between stacked label boxes in an elbow column.
quantities

a logical, vector, or list. Vectors are assumed to be text for the quantities' labels, which by default are the original values in the input to euler(). In addition to plain vectors, quantities$labels can also be a named vector keyed by subset names (e.g., "A", "B", "A&B"), which is useful for supplying custom text for overlap regions. If quantities$labels is NULL, quantities$format can be used to control number formatting as a list with an item fun (a function such as signif() or round()) and optional extra arguments passed to that function (for example, list(fun = prettyNum, big.mark = ",")). quantities$total can be used to set an external denominator for percent/fraction quantities (instead of the plotted total). to arguments that apply to grid::grid.text(), an argument type may also be used which should be a combination of "counts", "percent", and "fraction". The first item will be printed first and the second will be printed thereafter inside brackets. The default is type = "counts". For finer control over the rendered text, set quantities$template to a string with {counts}, {percent}, and/or {fraction} placeholders, for example "{counts}\n{percent}" to put the count and percentage on separate lines or "n={counts} ({percent})" for arbitrary layout. When template is set it overrides type; the set of placeholders in the template determines which values are computed.
annotations

free-form per-region text rendered as a third stacked element below the quantity (or below the label when no quantity is drawn). Accepts a named character vector keyed by subset name (e.g. c(A = "n = 12", "A&B" = "n = 3")) as a shorthand for ⁠list(labels = <vector>)⁠, or a list with labels plus grid::gpar() fields (col, alpha, fontsize, cex, fontfamily, lineheight, font, rot). Regions absent from labels are not annotated. The composite tag bbox grows to include the annotation, so exterior placement and leader lines adapt automatically. Defaults to slightly smaller text than labels / quantities (cex = 0.8).
strips

a list, ignored unless the 'by' argument was used in euler(). In addition to graphical parameters, this argument can include labels = list(top = ..., left = ...) for custom strip labels. Unnamed labels are interpreted in display order. Named labels are matched by factor levels and then reordered to display order.
bg

a logical, character, or list controlling the background grob. Character values are interpreted as the background fill color.
main

a title for the plot in the form of a character, expression, list or something that can be sensibly converted to a label via grDevices::as.graphicsAnnot(). A list of length one can be provided, in which case its only element is used as the label. If a list of longer length is provided, an item named 'label' must be provided (and will be used for the actual text).
complement

a logical, character, or list controlling the container box and complement region for diagrams fit with ⁠complement =⁠ in euler(). TRUE (default) draws the container with a dashed outline (lty = 2), no fill, and the complement count inside the complement region. FALSE suppresses the container and its label entirely. A character value is treated as a fill color shorthand. A list accepts fill, alpha, col, lty, lwd, lex (outline + label gpar), fontsize, cex, font, fontfamily, lineheight (label only), and label (custom text — defaults to the complement count). Also accepts the same placement controls as labels (placement, margin, tether, gap, leader, force_directed, elbow) for the complement count label. Has no effect if the diagram was fit without ⁠complement =⁠. Defaults can be set via eulerr_options(complement = ...).
rotate

a numeric value giving the angle in degrees by which to rotate the entire diagram layout. Positive values rotate counter-clockwise. Defaults to 0 (no rotation).
n

number of vertices for the edges and fills
adjust_labels

a logical. If TRUE, adjustment will be made to avoid overlaps or out-of-limits plotting of labels, quantities, and percentages.
...

parameters to update fills and edges with and thereby a shortcut to set these parameters grid::grid.text().

Details

The only difference between plot.euler() and plot.venn() is that quantities is set to TRUE by default in the latter and FALSE in the former.

Most of the arguments to this function accept either a logical, a vector, or a list where

  • logical values set the attribute on or off,

  • vectors are shortcuts to commonly used options (see the individual parameters), and

  • lists enable fine-grained control, including graphical parameters as described in grid::gpar() and control arguments that are specific to each argument.

The various grid::gpar() values that are available for each argument are:

fills edges labels quantities annotations strips legend main
col x x x x x x x
fill x
alpha x x x x x x x x
lty x
lwd x
lex x
fontsize x x x x x x
cex x x x x x x
fontfamily x x x x x x
lineheight x x x x x x
font x x x x x x

Defaults for these values, as well as other parameters of the plots, can be set globally using eulerr_options().

If the diagram has been fit using the data.frame or matrix methods and using the by argument, the plot area will be split into panels for each combination of the one to two factors. The fills, patterns, edges, labels, quantities, and annotations arguments each accept an optional by_group entry: a named list of override lists keyed by panel name (the names of the fitted object). For multi-by fits the panel name is the levels joined by ., e.g. "Male.German". Panels not listed in by_group use the top-level settings unchanged. Only graphical fields (and rot for labels, quantities, and annotations) may be overridden per panel; structural fields such as quantities$type, quantities$format, annotations$labels, or named-by-subset fills$fill must be set at the top level.

For users who are looking to plot their diagram using another package, all the necessary parameters can be collected if the result of this function is assigned to a variable (rather than printed to screen).

Value

Provides an object of class 'eulergram' , which is a description of the diagram to be drawn. plot.eulergram() does the actual drawing of the diagram.

See Also

euler(), plot.eulergram(), grid::gpar(), grid::grid.polyline(), grid::grid.path(), grid::grid.legend(), grid::grid.text()

Examples

fit <- euler(c("A" = 10, "B" = 5, "A&B" = 3))

# Customize colors, remove borders, bump alpha, color labels white
plot(fit,
     fills = list(fill = c("red", "steelblue4"), alpha = 0.5),
     labels = list(col = "white", font = 4))

# Add quantities to the plot
plot(fit, quantities = TRUE)

# Add free-form per-region annotations below the counts
plot(
  fit,
  quantities = TRUE,
  annotations = c(A = "mean = 35", "A&B" = "mean = 41")
)

# Add a custom legend and retain quantities
plot(fit, quantities = TRUE, legend = list(labels = c("foo", "bar")))

# Plot without fills and distinguish sets with border types instead
plot(fit, fills = "transparent", lty = 1:2)

# Save plot parameters to plot using some other method
diagram_description <- plot(fit)

# Plots using 'by' argument
plot(euler(fruits[, 1:4], by = list(sex)), legend = TRUE)

# Per-panel styling with `by_group`
plot(
  venn(fruits[, 1:4], by = list(sex)),
  quantities = list(
    by_group = list(
      male = list(col = "steelblue"),
      female = list(col = "tomato")
    )
  )
)

Print (plot) Euler diagram

Description

This function is responsible for the actual drawing of 'eulergram' objects created through plot.euler(). print.eulergram() is an alias for plot.eulergram(), which has been provided so that plot.euler() gets called automatically.

Usage

## S3 method for class 'eulergram'
plot(x, newpage = TRUE, ...)

## S3 method for class 'eulergram'
print(x, ...)

Arguments

x

an object of class 'eulergram', usually the output of plot.euler()
newpage

if TRUE, opens a new page via grid.newpage() to draw on
...

ignored

Value

A plot is drawn on the current device using grid::Grid() graphics.

Print a summary of an Euler diagram

Description

This function is responsible for printing fits from euler() and provides a summary of the fit. Prints a data frame of the original set relationships and the fitted values as well as diagError and stress statistics.

Usage

## S3 method for class 'euler'
print(x, round = 3, vsep = strrep("-", 0.75 * getOption("width")), ...)

Arguments

x

'euler' object from euler()
round

number of decimal places to round to
vsep

character string to paste in between euler objects when x is a nested euler object
...

arguments passed to base::print.data.frame()

Value

Summary statistics of the fitted Euler diagram are printed to screen.

See Also

euler(), base::print.data.frame()

Examples

euler(organisms)

Print a summary of a Venn diagram

Description

This function is responsible for printing objects from from venn() and provides a simple description of the number of sets and the specifications for the ellipses of the Venn diagram.

Usage

## S3 method for class 'eulerr_venn'
print(x, round = 3, vsep = strrep("-", 0.75 * getOption("width")), ...)

## S3 method for class 'venn'
print(...)

Arguments

x

an object of class 'eulerr_venn'
round

number of digits to round the ellipse specification to
vsep

character string to paste in between euler objects when x is a nested euler object
...

arguments passed to base::print.data.frame()

Value

Summary statistics of the fitted Venn diagram are printed to screen.

See Also

venn(), base::print.data.frame()

Examples

venn(organisms)

Residuals of euler object

Description

Residuals of euler object

Usage

## S3 method for class 'euler'
residuals(object, dense = FALSE, ...)

Arguments

object

object of class 'euler'
dense

same meaning as in fitted.euler()
...

ignored

Value

A named numeric vector of residuals (input minus fit) keyed by combination label.

Venn diagrams

Description

This function fits Venn diagrams using an interface that is almost identical to euler(). Strictly speaking, Venn diagrams are Euler diagrams where every intersection is visible, regardless of whether or not it is zero. In almost every incarnation of Venn diagrams, however, the areas in the diagram are also non-proportional to the input; this is also the case here.

Usage

venn(combinations, ...)

## Default S3 method:
venn(
  combinations,
  input = c("disjoint", "union"),
  names = letters[length(combinations)],
  ...
)

## S3 method for class 'table'
venn(combinations, ...)

## S3 method for class 'data.frame'
venn(
  combinations,
  weights = NULL,
  by = NULL,
  sep = "_",
  factor_names = TRUE,
  ...
)

## S3 method for class 'matrix'
venn(combinations, ...)

## S3 method for class 'list'
venn(combinations, ...)

Arguments

combinations

set relationships as a named numeric vector, matrix, or data.frame (see methods (by class))
...

arguments passed down to other methods
input

type of input: disjoint identities ('disjoint') or unions ('union').
names

a character vector for the names of each set of the same length as 'combinations'. Must not be NULL if combinations is a one-length numeric.
weights

a numeric vector of weights of the same length as the number of rows in combinations.
by

a factor or character matrix to be used in base::by() to split the data.frame or matrix of set combinations
sep

a character to use to separate the dummy-coded factors if there are factor or character vectors in 'combinations'.
factor_names

whether to include factor names when constructing dummy codes

Value

Returns an object of class ⁠'eulerr_venn', 'venn', 'euler'⁠ with items

shapes

a data frame of the precomputed ellipse parameters (one row per set, columns ⁠type, h, k, a, b, phi⁠). venn() always uses ellipses.
ellipses

the legacy 5-column data frame (⁠h, k, a, b, phi⁠) — kept for back-compat alongside the canonical shapes slot.
original.values

set relationships in the input
fitted.values

set relationships in the solution

Methods (by class)

  • venn(default): a named numeric vector, with combinations separated by an ampersand, for instance A&B = 10. Missing combinations are treated as being 0.

  • venn(table): A table with max(dim(x)) < 3.

  • venn(data.frame): a data.frame of logicals, binary integers, or factors.

  • venn(matrix): a matrix that can be converted to a data.frame of logicals (as in the description above) via base::as.data.frame.matrix().

  • venn(list): a list of vectors, each vector giving the contents of that set (with no duplicates). Vectors in the list do not need to be named.

See Also

plot.eulerr_venn(), print.eulerr_venn(), euler()

Examples

# The trivial version
f1 <- venn(5, names = letters[1:5])
plot(f1)

# Using data (a numeric vector)
f2 <- venn(c(A = 1, "B&C" = 3, "A&D" = 0.3))

# The table method
venn(pain, factor_names = FALSE)

# Using grouping via the 'by' argument through the data.frame method
venn(fruits, by = list(sex, age))


# Using the matrix method
venn(organisms)

# Using weights
venn(organisms, weights = c(10, 20, 5, 4, 8, 9, 2))

# A venn diagram from a list of sample spaces (the list method)
venn(plants[c("erigenia", "solanum", "cynodon")])