Area-Proportional Euler and Venn Diagrams with Circles or Ellipses

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.


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eulerr generates area-proportional Euler diagrams that display set relationships (intersections, unions, and disjoints) with circles or ellipses. Euler diagrams are Venn diagrams without the requirement that all set interactions be present (whether they are empty or not), which means that, depending on input, eulerr sometimes produces Venn diagrams and sometimes not.

With three or more sets intersecting, exact Euler diagrams are often impossible. For such cases eulerr attempts to provide a good approximation by numerically tuning the parameters of the ellipses or circles to minimize the error in the resulting diagram. Residuals and goodness of fit statistics are provided to assess whether the resulting diagram can be trusted.

Installation

install.packages("eulerr")

Development version

devtools::install_github("jolars/eulerr")

Shiny app

eulerr is also available as a shiny app hosted at jolars.co/eulerr.

Usage

library(eulerr)
# From Wilkinson 2012
fit <- euler(c("A" = 4, "B" = 6, "C" = 3, "D" = 2, "E" = 7, "F" = 3,
               "A&B" = 2, "A&F" = 2, "B&C" = 2, "B&D" = 1,
               "B&F" = 2, "C&D" = 1, "D&E" = 1, "E&F" = 1,
               "A&B&F" = 1, "B&C&D" = 1),
             shape = "ellipse")

We can inspect the goodness-of-fit metrics diagError and stress for the solution,

fit$stress
#> [1] 3.762385e-12
fit$diagError
#> [1] 3.944839e-07

and plot it

plot(fit)

Please see the introductory vignette for a brief introduction or eulerr under the hood for details.

License

eulerr is open source software, licensed under GPL-3.

Versioning

eulerr uses semantic versioning.

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Acknowledgements

eulerr would not be possible without Ben Frederickson's work on venn.js or Leland Wilkinson's venneuler.

News

eulerr 4.0.0

Major changes

  • plot.euler() has been rewritten completely from scratch, now using a custom grid-based implementation rather than lattice. As a result, all panel.*() functions and label() have been deprecated as well as arguments fill_alpha, auto.key, fontface, par.settings, default.prepanel, default.scales, and panel. The method for plotting diagrams has also changed---rather than overlaying shapes on top of each other, the diagram is now split into separate polygons using the polyclip package. Instead of relying on semi-transparent fills, the colors of the fills are now blended in the CIELab color space (#16).
  • The default color palette has been resdesigned from scratch to suit the new plot method.
  • A new function eulerr_options() have been provided in order to set default grahical parameters for the diagrams.

Minor changes

  • Arguments counts and outer_strips to plot.euler() are now defunct.
  • euler() now always returns ellipse-based parameters with columns h, k, a, b, and phi, regardless of which shape is used. This item was previously named "coefficients", but it now called "ellipses" instead and a custom coef.euler() method has been added to make cure that coef() still works.
  • Layouts are now partially normalized so that diagrams will look approximately the same even with different random seeds.

Bug fixes

  • Providing custom labels to quantities and labels arguments of plot.euler() now works correctly (#20).

eulerr 3.1.0

Major changes

  • The last-ditch optimizer switched from GenSA::GenSA() to RcppDE::DEoptim().
  • The optimizer used in all the remaining cases, including all circular diagrams and initial layouts, was switched back to stats::nlm() again.
  • In final optimization, we now use stress instead of residual sums of squares as a target for our optimizer.

Minor changes

  • label is now a proper generic with an appropriate method (label.euler()).
  • The eulerr under the hood vignette has received a substantial update.

Bug fixes

  • Fixed warnings resulting from the deprecated counts argument in one of the vignettes.
  • Fixed memcheck errors in the final optimizer.
  • Corrected erroneous labeling when auto.key = TRUE and labels were not in alphabetic order. (#15)

eulerr 3.0.1

Bug fixes

  • Added the missing %\VignetteEngine{knitr::knitr} to both vignettes. It had mistakenly been left out, which had mangled the resulting vignettes.

eulerr 3.0.0

Major changes

  • Ellipses are now supported by setting the new argument shape = "ellipse" in euler(). This functionality accompanies an overhaul of the innards of the function.
  • Initial optimization function and gradient have been ported to C++.
  • The initial optimizer has been switched from stats::optim(..., method = "L-BFGS-B") to stats::nlminb().
  • The final optimizer now falls back to GenSA::GenSA() when the fit from nlminb() isn't good enough, by default for 3 sets and ellipses, but this behavior can be controlled via a new argument control.
  • A packing algorithm has been introduced to arrange disjoint clusters of ellipses/circles.
  • The label placement algorithm has been rewritten to handle ellipses and been ported to C++. It now uses numerical optimization, which should provide slightly more accurate locations.
  • The initial optimizer now uses an analytical Hessian in addition to gradient.

Minor changes

  • The initial optimizer now restarts up to 10 times and picks the best fit (unless it is perfect somewhere along the way).
  • The default palette has been changed to a fixed palette, still adapted to color deficiency, but with some manual adjustments to, among other things, avoid unnecessary use of color.
  • The names of the diagError and regionError metrics have been changed from diag_error and region_error to reflect the original names.
  • The coordinates for the centers are now called h and k instead of x and y, respectively.
  • A new label() function has been added to extract locations for the overlaps for third party plotting (#10).
  • The counts argument to plot.euler() and panel.euler.labels() have been deprecated in favor of the more appropriate quantities.
  • Argument fill_opacity in plot.euler() that was deprecated in v2.0.0 has been made defunct.

eulerr 2.0.0

Major changes

  • eulerr() has been replaced with euler() (see update 1.1.0) and made defunct.
  • There are two new methods for euler:
    • euler.list() produces diagrams from a list of sample spaces.
    • euler.table() produces diagrams from a table object, as long as there are no dimensions with values greater than 2.
  • plot.euler() has been rewritten (again) from the ground up to better match other high-level functions from lattice. This change is intended to be as smooth as possible and should not make much of a difference to most users.
  • Arguments polygon_args, mar, and text_args to plot.euler() have been made defunct.

Minor changes

  • plot.euler() handles conflicting arguments better.
  • c++ routines in eulerr now use registration.
  • euler() now allows single sets (#9).
  • Labels in plot.euler() now use a bold fontface by default in order to distinguish them from the typeface used for counts.
  • Argument key in plot.euler() has been deprecated and replaced with auto.key. Notice that using key does not throw a warning since the argument is used in lattice::xyplot() (which plot.euler() relies on).
  • Argument fill_opacity is softly deprecated and has been replaced with fill_alpha for consistency with other lattice functions.

Bug fixes

  • border argument in plot.euler() works again (#7).

eulerr 1.1.0

Major changes

  • eulerr() and its related methods been deprecated and are being replaced by euler(), which takes slightly different input. Notably, the default is now to provide input in the form of disjoint class combinations, rather than unions. This is partly to make the function a drop-in replacement for venneuler::venneuler.
  • plot.euler() has been completely revamped, now interfacing xyplot() from lattice. As a result, arguments polygon_args, mar, and text_args have been deprecated.

Minor changes

  • Added a counts argument to plot.eulerr, which intersections and complements with counts from the original set specificiation (#6).
  • Added a key argument to plot.eulerr that prints a legend next to the diagram.
  • Switched to atan2() from RcppArmadillo.
  • Added version requirement for RcppArmadillo.
  • Dropped dependency on MASS for computing label placement, replacing it with a faster, geometric algorithm.
  • Dropped the cost function argument cost and now forces the function to use sums of squares, which is more or less equivalent to the cost function from venneuler.
  • Color palettes in plot.euler() now chooses colors adapted to color vision deficiency (deuteranopia). With increasingly large numbers of sets, this adaptation is relaxed to make sure that colors are kept visually distinct.
  • euler() now uses nlm() instead of optim(method = "Nelder-Mead") for its final optimization.

Bug fixes

  • The previous algorithm incorrectly computed loss from unions of sets. It now computes loss from disjoint class combinations.
  • Added missing row breaks in print.eulerr.

eulerr 1.0.0

New features

  • Final optimization routines have been completely rewritten in C++ using Rcpp and RcppArmadillo.
  • Switched to the cost function from EulerAPE for the default optimization target but added the posibility to choose cost function via a cost argument (currently eulerAPE or venneuler).
  • Added the option to produce conditional eulerr plots via a by argument to eulerr. The result is a list of euler diagrams that can be plotted in a grid arrangement via a new plot method.
  • Improved label placement by using a two-dimensional kernel density estimation instead of means to calculate label centers.

Bug fixes and minor improvements

  • Cleaned up typos and grammar errors in the Introduction to eulerr vignette.
  • Added mar argument to plot.eulerr with a default that produces symmetric margins.
  • Corrected the implementation of the stress statistic from venneuler.
  • Switched to Vogel sampling to generate points to choose label positions from.
  • Minor clean up and performance fixes all around.
  • Added a print.eulerr method.
  • Updated vignette to cover new features and changes.

eulerr 0.1.0

  • The first release.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("eulerr")

4.1.0 by Johan Larsson, 5 days ago


https://github.com/jolars/eulerr


Report a bug at https://github.com/jolars/eulerr/issues


Browse source code at https://github.com/cran/eulerr


Authors: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>), A. Jonathan R. Godfrey [ctb], Tim Kelley [ctb] (original Nelder-Mead code), David H. Eberly [ctb] (geometric algorithms), Peter Gustafsson [ctb], Emanuel Huber [ctb] (root solver code)


Documentation:   PDF Manual  


GPL-3 license


Imports graphics, grDevices, grid, lattice, polyclip, Rcpp, GenSA, stats, utils

Suggests covr, knitr, pBrackets, RConics, testthat

Linking to Rcpp, RcppArmadillo


See at CRAN