Package ‘eulerr’
June 20, 2017
Title Area-Proportional Euler Diagrams
Version 2.0.0
Description If possible, generates exactly area-proportional Euler diagrams,
or otherwise approximately proportional diagrams using numerical
optimization. A Euler diagram is a generalization of a Venn diagram,
relaxing the criterion that all interactions need to be represented.
Depends R (>= 3.3.1)
Imports graphics, grDevices, grid, stats, utils, assertthat, lattice,
Rcpp
Suggests knitr, rmarkdown, testthat
LinkingTo Rcpp (>= 0.12.8), RcppArmadillo (>= 0.7.600.1.0)
License GPL-3
Encoding UTF-8
LazyData true
VignetteBuilder knitr
URL https://github.com/jolars/eulerr
BugReports https://github.com/jolars/eulerr/issues
RoxygenNote 6.0.1
NeedsCompilation yes
Author Johan Larsson [aut, cre],
A. Jonathan R. Godfrey [ctb]
Maintainer Johan Larsson <[email protected]>
Repository CRAN
Date/Publication 2017-06-20 20:41:29 UTC
R topics documented:
euler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
eulerr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2
5
2
euler
panel.euler . . . .
panel.euler.circles
panel.euler.labels
plot.euler . . . .
prepanel.euler . .
print.euler . . . .
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Index
euler
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12
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.
Usage
euler(combinations, ...)
## Default S3 method:
euler(combinations, input = c("disjoint", "union"), ...)
## S3 method for class 'data.frame'
euler(combinations, weights = NULL, by = NULL, ...)
## 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 the
methods (by class) section for details.)
...
Arguments passed down to other methods.
input
The type of input: disjoint class combinations (disjoint) or unions (union).
weights
A numeric vector of weights of the same length as by and 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.
euler
3
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 sums of squared errors between the disjoint areas in the euler diagram
and the user’s input, namely
n
X
(yi − ŷi )2 ,
i=1
where ŷ are estimates of y that are currently being explored.
The stress statistic from venneuler is returned to give an indication of the goodness of the fit:
Pn
(y − ŷ )2
i=1
Pn i 2 i ,
i=1 yi
where ŷ are ordinary least squares estimates from the regression of the fitted areas on the original
areas that are currently being explored.
euler() also returns diag_error and region_error from eulerAPE. region_error is computed
as
yi
P − Pŷi .
yi
ŷi diag_error is simply the maximum of region_error.
Value
A list object of class ’euler’ with the following parameters.
coefficients
A matrix of x and y coordinates for the centers of the circles and their radii.
original.values
Set relationships provided by the user.
fitted.values Set relationships in the solution.
residuals
Residuals.
diag_error
The largest absolute residual in percentage points between the original and fitted
areas.
stress
The stress of the solution, computed as the sum of squared residuals over the
total sum of squares.
Methods (by class)
• default: A named numeric vector, with combinations separated by an ampersand, for instance A&B = 10. Missing combinations are treated as being 0.
• data.frame: A data.frame of logicals, two-level factors (see examples).
• matrix: A matrix that can be converted to a data.frame of logicals (as in the description above)
via base::as.data.frame.matrix().
• table: A table with max(dim(x)) < 3.
• list: A list of vectors, each vector giving the contents of that set. Vectors in the list do not
need to be named.
4
euler
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: http://doi.org/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: http://dx.
doi.org/10.1371/journal.pone.0101717
See Also
plot.euler(), print.euler()
Examples
# First fit the euler specification
fit <- euler(c("A" = 1, "B" = 0.4, "C" = 3, "A&B" = 0.2))
# Then plot it
plot(fit)
# Same result as above
euler(c("A" = 1, "B" = 0.4, "C" = 3,
"A&B" = 0.2, "A&C" = 0, "B&C" = 0,
"A&B&C" = 0))
# A euler diagram from a list of sample spaces (the list method)
euler(list(A = c("a", "ab", "ac", "abc"),
B = c("b", "ab", "bc", "abc"),
C = c("c", "ac", "bc", "abc")))
# Using the matrix method
mat <- cbind(A = sample(c(TRUE, TRUE, FALSE), size = 50, replace = TRUE),
B = sample(c(TRUE, FALSE), size = 50, replace = TRUE))
euler(mat)
# Using grouping via the 'by' argument
dat <- data.frame(
A = sample(c(TRUE, FALSE), size = 100, replace = TRUE),
B = sample(c(TRUE, TRUE, FALSE), size = 100, replace = TRUE),
gender = sample(c("Men", "Women"), size = 100, replace = TRUE),
nation = sample(c("Sweden", "Denmark"), size = 100, replace = TRUE)
)
euler(dat[, 1:2], by = dat[, 3:4])
# 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))
# The table method
eulerr
5
plot(euler(as.table(apply(Titanic, 2:4, sum))))
eulerr
Area-Proportional Euler Diagrams (defunct)
Description
Note: This function is defunct; please use euler() instead.
Usage
eulerr(...)
Arguments
...
Ignored
panel.euler
Panel Function for Euler Diagrams
Description
Panel Function for Euler Diagrams
Usage
panel.euler(x, y, r, subscripts, fill = superpose.polygon$col,
lty = superpose.polygon$lty, lwd = superpose.polygon$lwd,
border = superpose.polygon$border, alpha = superpose.polygon$alpha,
fontface = "bold", counts = TRUE, labels = NULL, original.values,
fitted.values, ...)
Arguments
x
X coordinates for the circle centers.
y
Y coordinates for the circle centers.
r
Radii.
subscripts
A vector of subscripts (See lattice::xyplot()).
fill
Fill color for circles. (See grid::gpar().)
lty
Line type for circles. (See grid::gpar().)
lwd
Line weight for circles. (See grid::gpar().)
border
Border color for circles.
6
panel.euler.circles
alpha
Alpha for circles. Note that plot.euler() by default modifies the alpha of col
instead to avoid affecting the alpha of the borders. (See grid::gpar().)
fontface
Fontface for the labels. (See grid::gpar().)
counts
Plots the original values for the disjoint set combinations (original.values).
Can also be a list, in which the contents of the list will be passed on to lattice::panel.text()
to modify the appearance of the counts.
labels
Labels to plot on the circles.
original.values
Original values for the disjoint set combinations.
fitted.values
Fitted values for the disjoint set combinations.
...
Passed down to panel.euler.circles() and panel.euler.labels().
Value
Plots euler diagrams inside a trellis panel.
See Also
grid::gpar().
panel.euler.circles
Panel Function for Circles
Description
Panel Function for Circles
Usage
panel.euler.circles(x, y, r, border = "black", fill = "transparent", ...,
identifier = NULL, name.type = "panel", col, font, fontface)
Arguments
x
X coordinates for the circle centers.
y
Y coordinates for the circle centers.
r
Radii.
border
Border color.
fill
Circle fill.
...
Passed on to grid::grid.circle().
identifier
A character string that is prepended to the name of the grob that is created.
name.type
A character value indicating whether the name of the grob should have panel or
strip information added to it. Typically either "panel", "strip", "strip.left",
or "" (for no extra information).
panel.euler.labels
7
col
Ignored
font
Ignored
fontface
Ignored
Value
Plots circles inside a trellis panel.
See Also
grid::grid.circle().
panel.euler.labels
Panel Function for Circle Labels
Description
Panel Function for Circle Labels
Usage
panel.euler.labels(x, y, r, labels, counts = TRUE, original.values,
fitted.values, ...)
Arguments
x
X coordinates for the circle centers.
y
Y coordinates for the circle centers.
r
Radii.
labels
Labels to plot on the circles.
counts
Plots the original values for the disjoint set combinations (original.values).
Can also be a list, in which the contents of the list will be passed on to lattice::panel.text()
to modify the appearance of the counts.
original.values
Original values for the disjoint set combinations.
fitted.values
Fitted values for the disjoint set combinations.
...
Arguments passed on to panel.text()
Value
Computes and plots labels or counts inside the centers of the circles’ overlaps.
8
plot.euler
plot.euler
Plot Area-Proportional Euler Diagrams
Description
Plot Euler diagrams with trellis graphics from lattice. This function calls lattice::xyplot()
under the hood, allowing plots of both individual euler diagrams as well as grids of diagrams in
case the by argument was used in the call to euler().
Usage
## S3 method for class 'euler'
plot(x, fill = qualpalr_pal, fill_alpha = 0.4,
auto.key = FALSE, counts = FALSE, labels = is.logical(auto.key) &&
!isTRUE(auto.key), fontface = "bold", par.settings = list(), ...,
default.prepanel = prepanel.euler, default.scales = list(draw = FALSE),
panel = panel.euler, outer_strips, fill_opacity)
Arguments
x
An object of class euler.
fill
Fill color. Either a function that takes as its first argument the number of colors
to generate, or a sequence of colors.
fill_alpha
Alpha for the fill.
auto.key
Plot a legend for the sets.
counts
Plot counts.
labels
A list or character vector of labels.
fontface
Fontface for the labels. (See grid::gpar()).
par.settings
Graphical parameters for trellis displays. See lattice::trellis.par.get().
...
Arguments to pass down to panel.euler(), which in turn passes them down to
panel.euler.circles() and panel.euler.labels().
default.prepanel
Default prepanel function. Should usually be left untouched.
default.scales Default scales. Turns off
panel
The panel function. Should usually be left untouched.
outer_strips
Deprecated
fill_opacity
Deprecated
plot.euler
9
Details
Almost all of the relevant functionality for lattice::xyplot() is available here. For instance, providing specifications to par.settings will have an effect on many aspects of the plot. Moreover,
arguments that are given here will trickle down to the panel function panel.euler() and subsequently to panel.euler.circles() and panel.euler.labels(), which do the actual plotting.
The default value for fill causes, eulerr to choose color palettes based on the number of sets,
trying to provide palettes adapted to color vision deficiencies based on qualpalr::qualpal().
Value
An object of class "trellis". The update method can be used to update components of the object
and the print method (usually called by default) will plot it on an appropriate plotting device.
See Also
panel.euler.circles(), panel.euler.labels(), lattice::xyplot(), grid::gpar(), grid::grid.circle(),
lattice::panel.xyplot(), euler(), qualpalr::qualpal()
Examples
fit <- euler(c("A" = 10, "B" = 5, "A&B" = 3))
plot(fit, labels = c("foo", "bar"), fill_alpha = 0.7)
# Customize colors, remove borders, bump alpha, color labels white
plot(fit,
fill_alpha = 0.5,
fill = c("red", "steelblue4"),
col = "white",
border = "transparent",
fontface = "bold.italic")
# Add counts to the plot
plot(fit, counts = TRUE)
# Add a custom legend and retain counts
plot(fit, counts = TRUE, auto.key = list(space = "bottom", columns = 2))
# Plot without fills and distinguish sets with border types instead
plot(fit, lty = c("solid", "dotted"), fill = "transparent", cex = 2,
fontface = 2, labels = c("foo", "bar"))
# Plot a grid of euler plots
dat <- data.frame(
A
= sample(c(TRUE, FALSE), size = 100, replace = TRUE),
B
= sample(c(TRUE, TRUE, FALSE), size = 100, replace = TRUE),
gender = sample(c("Men", "Women"), size = 100, replace = TRUE),
nation = sample(c("Sweden", "Denmark"), size = 100, replace = TRUE)
)
gridfit <- euler(dat[, 1:2], by = dat[, 3:4])
plot(gridfit, auto.key = TRUE)
10
print.euler
# We can modify the grid layout as well
plot(gridfit, layout = c(1, 4))
prepanel.euler
Prepanel Function for Euler Diagrams
Description
Prepanel Function for Euler Diagrams
Usage
prepanel.euler(x, y, r, subscripts, ...)
Arguments
x
X coordinates for the circle centers.
y
Y coordinates for the circle centers.
r
Radii.
subscripts
A vector of subscripts (See lattice::xyplot()).
...
Ignored.
Value
A list of xlim and ylim items.
print.euler
Print Euler Fits
Description
Prints a data frame of the original set relationships and the fitted values as well as diag_error and
stress statistics.
Usage
## S3 method for class 'euler'
print(x, round = 3, ...)
Arguments
x
Euler diagram specification from euler().
round
Number of decimal places to round to.
...
Arguments passed to base::print.data.frame().
print.euler
Value
Prints the results of the fit.
11
Index
base::as.data.frame.matrix(), 3
base::by(), 2
base::print.data.frame(), 10
euler, 2
euler(), 5, 8–10
eulerr, 5
grid::gpar(), 5, 6, 8, 9
grid::grid.circle(), 6, 7, 9
lattice::panel.text(), 6, 7
lattice::panel.xyplot(), 9
lattice::trellis.par.get(), 8
lattice::xyplot(), 5, 8–10
panel.euler, 5
panel.euler(), 8, 9
panel.euler.circles, 6
panel.euler.circles(), 6, 8, 9
panel.euler.labels, 7
panel.euler.labels(), 6, 8, 9
panel.text(), 7
plot.euler, 8
plot.euler(), 4, 6
prepanel.euler, 10
print, 9
print.euler, 10
print.euler(), 4
qualpalr::qualpal(), 9
update, 9
12