NEWS.md

In eulerr: Area-Proportional Euler and Venn Diagrams with Ellipses

Changelog

eulerr 7.0.2

Bug Fixes

• Fix order and layout of strips when grouping (#108, by @altairwei)

eulerr 7.0.1

Minor Changes

• Fixed some incorrect documentation of internal functions.
• Corrected an url for eulerAPE.

eulerr 7.0.0

New Features

• It is now possible to set the loss function to be used when trying to optimize the Euler diagram layout via loss and loss_aggregator. There is a new vignette that showcases this new feature.

Minor Changes

• C++14 is now required for the package.

Bug Fixes

• Label repelling via adjust_labels in plot.euler() has been deprecated and removed to fix sanitizer warnings.

eulerr 6.1.1

Minor changes

• citation to conference paper added to inst/CITATION
• error messages for erroneous input have been improved in several places
• switched PI to M_PI to support STRICT_R_HEADERS in C++ code (#82, thanks @eddelbuettel)

Bug fixes

• error in documentation for list method has been fixed, thanks @gprezza (##77)

eulerr 6.1.0

Minor changes

• Label repelling (activated by calling euler() with adjust_labels = TRUE) no longer repels text labels away from the edges of the shapes in the diagram.

Bug fixes

• Rectify sanitizer error from clang-ASAN test environment.

eulerr 6.0.2

Bug fixes

• Set stringsAsFactors = TRUE inside all relevant functions in euler() to avoid errors in upcoming R version.
• Fix broken link in eulerr under the hood vignette.

eulerr 6.0.1

Minor changes

• Throw an error message when the number of sets in venn() exceeds 5 (##65)
• Performance improved when large lists are used as input to euler() and venn() (##64, @privefl)

Bug fixes

• Correctly handle data.frame inputs to euler() when categorical variables are character vectors and not factors.

eulerr 6.0.0

New features

• In plot.euler(), percentages can be added to the plot in addition to or instead of counts by providing a list to the quantities argument with an item type that can take any combination of counts and percent. This change also comes with a redesign of the grid graphics implementation for labels.
• eulerr_options() gains a new argument padding which controls the amount of padding between labels and quantities. (##48)
• plot.euler() now uses code from the ggrepel package to prevent labels from overlapping or escaping the plot area if adjust_labels is set to TRUE.
• A new vignette featuring a gallery of plots from the package has been added.

Minor changes

• The default cex for quantity labels has changed from 1.0 to 0.9.
• Labels for sets that overlap are now merged (partly fixes ##45)
• The fill colors for sets which are completely contained within another set are now once again composed of a mix of the color of the subset and the superset.
• Plotting data has been exposed in a data slot in the object created by calling to plot.euler() (##57)

Bug fixes

• An error in layout normalization that occurred sometimes with ellipses has been fixed.

eulerr 5.1.0

New features

• venn() is a new function that produces Venn diagrams for up to 5 sets. The interface is almost identical to euler() except that a single integer can also be provided. A new vignette, Venn diagrams with eulerr, exemplifies its use.

Minor changes

• Calculations for the strips in plot.euler() when a list of Euler diagrams is given has been improved. Setting fontsize or cex now results in appropriately sized strips as one would expect.
• Tiny overlaps (where the fraction of the area is less than one thousandth of the largest overlap) in the final diagram are no longer plotted.
• eulergram() objects from plot.euler() now have a proper grob name for the canvas grob, so that extracting information from them is easier.

Bug fixes

• Return value documentation for euler() now correctly says "ellipses" and not "coefficients".
• data.frame or matrix inputs now work properly when values are numerical. (##42)
• Fixed some spelling errors in news and vignettes.

eulerr 5.0.0

New features

• error_plot() is a new function that offers diagnostic plots of fits from euler(), letting the user visualize the error in the resulting Euler diagram.

Major changes

• euler() once again uses the residual sums of squares, rather than the stress metric, as optimization objective, which means that output is always scaled appropriately to input (##28).
• plot.euler() now uses the polylabelr package to position labels for the overlaps of the ellipses, which has improved performance in plotting complicated diagrams considerably and reduced the amount of code in this package greatly.
• The c++ internals have been rewritten using more memory-efficient, performant and expressive code.

Minor changes

• The euler.data.frame() method (and by proxy the euler.matrix() method) can now take matrices with factors in addition to the previously supported logical and integer (binary) input. The function will dummy code the variables for the user.
• A few performance fixes.
• Additional unit tests.
• Previously deprecated arguments to plot.euler() have been made defunct.
• Added a data set, plants, to exemplify the list method for euler().
• Added a data set, fruits, to exemplify the data.frame method for euler().
• euler.data.frame() gains an argument sep, which is a character vector used to separate dummy-coded factors if there are factors or characters in the input.
• Added a data set, organisms, to exemplify the matrix method for euler().
• Added a data set, pain, to exemplify the table method for euler().
• euler.table() gains an argument, factor_names, for specifying whether the factor names should be included when generating dummy-coded variables in case the input is a data.frame with character or factor vectors or if the input is a table with more than two columns or rows.
• Parts of the eulerr under the hood vignette has been branched off into a new vignette regarding visualization.

Bug fixes

• Empty combinations can now be provided and will be plotted (generating completely blank plots).
• euler.list() now passes its ellipsis argument along properly. (##33, thanks, @banfai)
• Several spelling and grammar mistakes were corrected in vignettes and documentation.

eulerr 4.1.0

Minor changes

• plot.euler() now returns a gTree object. All of the plotting mechanisms are now also found in this function and plot.eulergram() and print.eulergram() basically just call grid::grid.draw() on the result of plot.euler(). This change means that functions such as gridExtra::grid.arrange() now work as one would intuit on the objects produced by plot.euler().
• Fitting and plotting Euler diagrams with empty sets is now allowed (##23). Empty sets in the input will be returned as NA in the resulting data.frame of ellipses.
• The last-ditch optimizer has been switched back to GenSA::GenSA() from RcppDE::DEoptim().

Bug fixes

• The grid parameters available for edges are now correctly specified in the manual for plot.euler().
• euler.data.frame() now works as expected for tibbles (from the tibble package) when argument by is used.

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 redesigned from scratch to suit the new plot method.
• A new function eulerr_options() have been provided in order to set default graphical 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 font face 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 specification (##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 possibility 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.

eulerr documentation built on May 29, 2024, 1:35 a.m.