Constructs and draws a zigzag expanded navigation plot for a graphical exploratory analysis of a path of variables. The result is an alternating sequence of one-dimensional (1d) and two-dimensional (2d) plots laid out in a zigzag-like structure so that each consecutive pair of 2d plots has one of its variates (or coordinates) in common with that of the 1d plot appearing between them.
zenplot(x, turns = NULL,
first1d = TRUE, last1d = TRUE,
n2dcols = c("letter", "square", "A4", "golden", "legal"),
n2dplots = NULL,
plot1d = c("label", "points", "jitter", "density", "boxplot", "hist",
"rug", "arrow", "rect", "lines", "layout"),
plot2d = c("points", "density", "axes", "label", "arrow", "rect", "layout"),
zargs = c(x = TRUE, turns = TRUE, orientations = TRUE,
vars = TRUE, num = TRUE, lim = TRUE, labs = TRUE,
width1d = TRUE, width2d = TRUE,
ispace = match.arg(pkg) != "graphics"),
lim = c("individual", "groupwise", "global"),
labs = list(group = "G", var = "V", sep = ", ", group2d = FALSE),
pkg = c("graphics", "grid", "loon"),
method = c("tidy", "double.zigzag", "single.zigzag", "rectangular"),
width1d = if(is.null(plot1d)) 0.5 else 1,
width2d = 10,
ospace = if(pkg == "loon") 0 else 0.02,
ispace = if(pkg == "graphics") 0 else 0.037,
draw = TRUE,
...)Arguments
- x
A data object of "standard forms", being a
vector, or amatrix, or adata.frame, or alistof any of these. In the case of a list, the components ofxare interpreted as groups of data which are visually separated by a two-dimensional (group) plot.- turns
A
charactervector (of length two times the number of variables to be plotted minus 1) consisting of"d","u","r"or"l"indicating the turns out of the current plot position; ifNULL, theturnsare constructed (ifxis of the "standard form" described above).- first1d
A
logicalindicating whether the first one-dimensional plot is included.- last1d
A
logicalindicating whether the last one-dimensional plot is included.- n2dcols
number of columns of 2d plots (\(\ge 1\)) or one of
"letter","square","A4","golden"or"legal"in which case a similar layout is constructed. Note thatn2dcolsis ignored if!is.null(turns).- n2dplots
The number of 2d plots.
- plot1d
A
functionto use to return a one-dimensional plot constructed with packagepkg. Alternatively, acharacterstring of an existing function. For the defaults provided, the corresponding functions are obtained when appending_1d_graphics,_1d_gridor_1d_loondepending on whichpkgis used.If
plot1d = NULL, then no 1d plot is produced in thezenplot.- plot2d
A
functionreturning a two-dimensional plot constructed with packagepkg. Alternatively, acharacterstring of an existing function. For the defaults provided, the corresponding functions are obtained when appending_2d_graphics,_2d_gridor_2d_loondepending on whichpkgis used.As for
plot1d,plot2domits 2d plots ifplot2d = NULL.- zargs
A fully named
logicalvectorindicating whether the respective arguments are (possibly) passed toplot1d()andplot2d()(if the latter contain the formal argumentzargs, which they typically do/should, but see below for an example in which they do not).zargscan maximally contain all variables as given in the default. If one of those variables does not appear inzargs, it is treated asTRUEand the corresponding arguments are passed on toplot1dandplot2d. If one of them is set toFALSE, the argument is not passed on.- lim
(x-/y-)axis limits. This can be a
characterstring or anumeric(2).If
lim = "groupwise"andxdoes not contain groups, the behaviour is equivalent tolim = "global".- labs
The plot labels to be used; see the argument
labsofburst()for the exact specification.labscan, in general, be anything as long asplot1dandplot2dknow how to deal with it.- pkg
The R package used for plotting (depends on how the functions
plot1dandplot2dwere constructed; the user is responsible for choosing the appropriate package among the supported ones).- method
The type of zigzag plot (a
character).Available are:
tidy:more tidied-up
double.zigzag(slightly more compact placement of plots towards the end).double.zigzag:zigzag plot in the form of a flipped “S”. Along this path, the plots are placed in the form of an “S” which is rotated counterclockwise by 90 degrees.
single.zigzag:zigzag plot in the form of a flipped “S”.
rectangular:plots that fill the page from left to right and top to bottom. This is useful (and most compact) for plots that do not share an axis.
Note that
methodis ignored ifturnsare provided.- width1d
A graphical parameter > 0 giving the width of 1d plots.
- width2d
A graphical parameter > 0 giving the height of 2d plots.
- ospace
The outer space around the zenplot. A vector of length four (bottom, left, top, right), or one whose values are repeated to be of length four, which gives the outer space between the device region and the inner plot region around the zenplot.
Values should be in \([0,1]\) when
pkgis"graphics"or"grid", and as number of pixels whenpkgis"loon".- ispace
The inner space in \([0,1]\) between the each figure region and the region of the (1d/2d) plot it contains. Again, a vector of length four (bottom, left, top, right) or a shorter one whose values are repeated to produce a vector of length four.
- draw
A
logicalindicating whether a thezenplotis immediately displayed (the default) or not.- ...
arguments passed to the drawing functions for both
plot1dandplot2d. If you need to pass certain arguments only to one of them, say,plot2d, consider providing your ownplot2d; see the examples below.
Value
(besides plotting) invisibly returns a list having additional classnames marking it as a zenplot and a zenPkg object (with Pkg being one of Graphics, Grid, or Loon, so as to identify the package used to construct the plot).
As a list it contains at least
the path and layout (see unfold for details).
Depending on the graphics package pkg used, the returned list
includes additional components. For pkg = "grid",
this will be the whole plot as a grob (grid object).
For pkg = "loon", this will be the whole plot as a
loon plot object as
well as the toplevel tk object in which the plot appears.
See also
All provided default plot1d and plot2d functions.
extract_1d() and extract_2d()
for how zargs can be split up into a list of columns and corresponding
group and variable information.
burst() for how x can be split up into all sorts of
information useful for plotting (see our default plot1d and plot2d).
vport() for how to construct a viewport for
(our default) grid (plot1d and plot2d) functions.
extract_pairs(), connect_pairs(),
group() and zenpath() for
(zen)path-related functions.
The various vignettes for additional examples.
Other creating zenplots:
unfold()
Examples
### Basics #####################################################################
## Generate some data
n <- 1000 # sample size
d <- 20 # dimension
set.seed(271) # set seed (for reproducibility)
x <- matrix(rnorm(n * d), ncol = d) # i.i.d. N(0,1) data
## A basic zenplot
res <- zenplot(x)
uf <- unfold(nfaces = d - 1)
## `res` and `uf` is not identical as `res` has specific
## class attributes.
for(name in names(uf)) {
stopifnot(identical(res[[name]], uf[[name]]))
}
## => The return value of zenplot() is the underlying unfold()
## Some missing data
z <- x
z[seq_len(n-10), 5] <- NA # all NA except 10 points
zenplot(z)
## Another column with fully missing data (use arrows)
## Note: This could be more 'compactified', but is technically
## more involved
z[, 6] <- NA # all NA
zenplot(z)
## Lists of vectors, matrices and data frames as arguments (=> groups of data)
## Only two vectors
z <- list(x[,1], x[,2])
zenplot(z)
## A matrix and a vector
z <- list(x[,1:2], x[,3])
zenplot(z)
## A matrix, NA column and a vector
z <- list(x[,1:2], NA, x[,3])
zenplot(z)
z <- list(x[,1:2], cbind(NA, NA), x[,3])
zenplot(z)
z <- list(x[,1:2], 1:10, x[,3])
zenplot(z)
## Without labels or with different labels
z <- list(A = x[,1:2], B = cbind(NA, NA), C = x[,3])
zenplot(z, labs = NULL) # without any labels
zenplot(z, labs = list(group = NULL, group2d = TRUE)) # without group labels
zenplot(z, labs = list(group = NULL)) # without group labels unless groups change
zenplot(z, labs = list(var = NULL)) # without variable labels
zenplot(z, labs = list(var = "Variable ", sep = " - ")) # change default labels
## Example with a factor
zenplot(iris)
zenplot(iris, lim = "global") # global scaling of axis
zenplot(iris, lim = "groupwise") # acts as 'global' here (no groups in the data)
### More sophisticated examples ################################################
## Note: The third component (data.frame) naturally has default labels.
## zenplot() uses these labels and prepends a default group label.
z <- list(x[,1:5], x[1:10, 6:7], NA,
data.frame(x[seq_len(round(n/5)), 8:19]), cbind(NA, NA), x[1:10, 20])
zenplot(z, labs = list(group = "Group ")) # change the group label (var and sep are defaults)
## Alternatively, give z labels
names(z) <- paste("Group", LETTERS[seq_len(length(z))]) # give group names
zenplot(z) # uses given group names
## Now let's change the variable labels
z. <- lapply(z, function(z.) {
if(!is.matrix(z.)) z. <- as.matrix(z.)
colnames(z.) <- paste("Var.", seq_len(ncol(z.)))
z.
}
)
zenplot(z.)
### A dynamic plot based on 'loon' (if installed and R compiled with tcl support)
if (FALSE) {
if(requireNamespace("loon", quietly = TRUE))
zenplot(x, pkg = "loon")
}
### Providing your own turns ###################################################
## A basic example
turns <- c("l","d","d","r","r","d","d","r","r","u","u","r","r","u","u","l","l",
"u","u","l","l","u","u","l","l","d","d","l","l","d","d","l","l",
"d","d","r","r","d","d")
zenplot(x, plot1d = "layout", plot2d = "layout", turns = turns) # layout of plot regions
## => The tiles stick together as ispace = 0.
zenplot(x, plot1d = "layout", plot2d = "layout", turns = turns,
pkg = "grid") # layout of plot regions with grid
## => Here the tiles show the small (default) ispace
## Another example (with own turns and groups)
zenplot(list(x[,1:3], x[,4:7]), plot1d = "arrow", plot2d = "rect",
turns = c("d", "r", "r", "r", "r", "d",
"d", "l", "l", "l", "l", "l"), last1d = FALSE)
### Providing your own plot1d() or plot2d() ####################################
## Creating a box
zenplot(x, plot1d = "label", plot2d = function(zargs)
density_2d_graphics(zargs, box = TRUE))
## With grid
# \donttest{
zenplot(x, plot1d = "label", plot2d = function(zargs)
density_2d_grid(zargs, box = TRUE), pkg = "grid")
# }
## An example with width1d = width2d and where no zargs are passed on.
## Note: This could have also been done with 'rect_2d_graphics(zargs, col = ...)'
## as plot1d and plot2d.
myrect <- function(...) {
plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, ylim = 0:1)
rect(xleft = 0, ybottom = 0, xright = 1, ytop = 1, ...)
}
zenplot(matrix(0, ncol = 15),
n2dcol = "square", width1d = 10, width2d = 10,
plot1d = function(...) myrect(col = "royalblue3"),
plot2d = function(...) myrect(col = "maroon3"))
## Colorized rugs as plot1d()
basecol <- c("royalblue3", "darkorange2", "maroon3")
palette <- colorRampPalette(basecol, space = "Lab")
cols <- palette(d) # different color for each 1d plot
zenplot(x, plot1d = function(zargs) {
rug_1d_graphics(zargs, col = cols[(zargs$num+1)/2])
}
)
## With grid
library(grid) # for gTree() and gList()
# \donttest{
zenplot(x, pkg = "grid", # you are responsible for choosing the right pkg (cannot be tested!)
plot1d = function(zargs)
rug_1d_grid(zargs, col = cols[(zargs$num+1)/2]))
# }
## Rectangles with labels as plot2d() (shows how to overlay plots)
## With graphics
## Note: myplot2d() could be written directly in a simpler way, but is
## based on the two functions here to show how they can be combined.
zenplot(x, plot1d = "arrow", plot2d = function(zargs) {
rect_2d_graphics(zargs)
label_2d_graphics(zargs, add = TRUE)
})
## With grid
# \donttest{
zenplot(x, pkg = "grid", plot1d = "arrow", plot2d = function(zargs)
gTree(children = gList(rect_2d_grid(zargs),
label_2d_grid(zargs))))
# }
## Rectangles with labels outside the 2d plotting region as plot2d()
## With graphics
zenplot(x, plot1d = "arrow", plot2d = function(zargs) {
rect_2d_graphics(zargs)
label_2d_graphics(zargs, add = TRUE, xpd = NA, srt = 90,
loc = c(1.04, 0), adj = c(0,1), cex = 0.7)
})
## With grid
# \donttest{
zenplot(x, pkg = "grid", plot1d = "arrow", plot2d = function(zargs)
gTree(children = gList(rect_2d_grid(zargs),
label_2d_grid(zargs, loc = c(1.04, 0),
just = c("left", "top"),
rot = 90, cex = 0.45))))
# }
## 2d density with points, 1d arrows and labels
zenplot(x, plot1d = function(zargs) {
rect_1d_graphics(zargs)
arrow_1d_graphics(zargs, add = TRUE, loc = c(0.2, 0.5))
label_1d_graphics(zargs, add = TRUE, loc = c(0.8, 0.5))
}, plot2d = function(zargs) {
points_2d_graphics(zargs, col = adjustcolor("black", alpha.f = 0.4))
density_2d_graphics(zargs, add = TRUE)
})
## 2d density with labels, 1d histogram with density and label
## Note: The 1d plots are *improper* overlays here as the density
## plot does not know the heights of the histogram. In other
## words, both histograms and densities use the whole 1d plot
## region but are not correct relative to each other in the
## sense of covering the same are. For a *proper* overlay
## see below.
zenplot(x,
plot1d = function(zargs) {
hist_1d_graphics(zargs)
density_1d_graphics(zargs, add = TRUE,
border = "royalblue3",
lwd = 1.4)
label_1d_graphics(zargs, add = TRUE,
loc = c(0.2, 0.8),
cex = 0.6, font = 2,
col = "darkorange2")
},
plot2d = function(zargs) {
density_2d_graphics(zargs)
points_2d_graphics(zargs, add = TRUE,
col = adjustcolor("black", alpha.f = 0.3))
}
)
### More sophisticated examples ################################################
### Example: Overlaying histograms with densities (the *proper* way)
# \donttest{
## Define proper 1d plot for overlaying histograms with densities
hist_with_density_1d <- function(zargs)
{
## Extract information and data
num <- zargs$num # plot number (among all 1d and 2d plots)
turn.out <- zargs$turns[num] # turn out of current position
horizontal <- turn.out == "d" || turn.out == "u"
# the indices of the 'x' variable to be displayed in the current plot
ii <- plot_indices(zargs)
label <- paste0("V", ii[1]) # label
srt <- if(horizontal) 0 else if(turn.out == "r") -90 else 90 # label rotation
x <- zargs$x[,ii[1]] # data
lim <- range(x) # data limits
## Compute histogram information
breaks <- seq(from = lim[1], to = lim[2], length.out = 21)
binInfo <- hist(x, breaks = breaks, plot = FALSE)
binBoundaries <- binInfo$breaks
widths <- diff(binBoundaries)
heights <- binInfo$density
## Compute density information
dens <- density(x)
xvals <- dens$x
keepers <- (min(x) <= xvals) & (xvals <= max(x)) # keep those within the range of the data
x. <- xvals[keepers]
y. <- dens$y[keepers]
## Determine plot limits and data
if(turn.out == "d" || turn.out == "l") { # flip density/histogram
heights <- -heights
y. <- -y.
}
if(horizontal) {
xlim <- lim
xlim.bp <- xlim - xlim[1] # special for barplot(); need to shift the bars
ylim <- range(0, heights, y.)
ylim.bp <- ylim
x <- c(xlim[1], x., xlim[2]) - xlim[1] # shift due to plot region set up by barplot()
y <- c(0, y., 0)
} else {
xlim <- range(0, heights, y.)
xlim.bp <- xlim
ylim <- lim
ylim.bp <- ylim - ylim[1] # special for barplot(); need to shift the bars
x <- c(0, y., 0)
y <- c(xlim[1], x., xlim[2]) - ylim[1] # shift due to plot region set up by barplot()
}
## Determining label position relative to the zenpath
loc <- c(0.1, 0.6)
# when walking downwards, change both left/right and up/down
if(turn.out == "d") loc <- 1-loc
# when walking to the right, coordinates change and 2nd is flipped
if(turn.out == "r") {
loc <- rev(loc)
loc[2] <- 1-loc[2]
}
# when walking to the left, coordinates change and 1st is flipped
if(turn.out == "l") {
loc <- rev(loc)
loc[1] <- 1-loc[1]
}
## Plotting
barplot(heights, width = widths, xlim = xlim.bp, ylim = ylim.bp,
space = 0, horiz = !horizontal, main = "", xlab = "", axes = FALSE) # histogram
polygon(x = x, y = y, border = "royalblue3", lwd = 1.4) # density
opar <- par(usr = c(0, 1, 0, 1)) # switch to relative coordinates for text
on.exit(par(opar))
text(x = loc[1], y = loc[2], labels = label, cex = 0.7, srt = srt, font = 2,
col = "darkorange2") # label
}
## Zenplot
zenplot(x,
plot1d = "hist_with_density_1d",
plot2d = function(zargs) {
density_2d_graphics(zargs)
points_2d_graphics(zargs,
add = TRUE,
col = adjustcolor("black", alpha.f = 0.3))
}
)
#> Error in zenplot(x, plot1d = "hist_with_density_1d", plot2d = function(zargs) { density_2d_graphics(zargs) points_2d_graphics(zargs, add = TRUE, col = adjustcolor("black", alpha.f = 0.3))}): Function provided as argument 'plot1d' does not exist.
# }
### Example: A path through pairs of a grouped t copula sample
# \donttest{
## 1) Build a random sample from a 17-dimensional grouped t copula
d. <- c(8, 5, 4) # sector dimensions
d <- sum(d.) # total dimension
nu <- rep(c(12, 1, 0.25), times = d.) # d.o.f. for each dimension
n <- 500 # sample size
set.seed(271)
Z <- matrix(rnorm(n * d), ncol = n) # (d,n)-matrix
P <- matrix(0.5, nrow = d, ncol = d)
diag(P) <- 1
L <- t(chol(P)) # L: LL^T = P
Y <- t(L %*% Z) # (n,d)-matrix containing n d-vectors following N(0,P)
U. <- runif(n)
W <- sapply(nu, function(nu.) 1/qgamma(U., shape = nu./2, rate = nu./2)) # (n,d)-matrix
X <- sqrt(W) * Y # (n,d)-matrix
U <- sapply(1:d, function(j) pt(X[,j], df = nu[j])) # (n,d)-matrix
## 2) Plot the data with a pairs plot, colorizing the groups
cols <- matrix("black", nrow = d, ncol = d) # colors
start <- c(1, cumsum(head(d., n = -1))+1) # block start indices
end <- cumsum(d.) # block end indices
for(j in seq_along(d.)) cols[start[j]:end[j], start[j]:end[j]] <- basecol[j] # colors
diag(cols) <- NA # remove colors corresponding to diagonal entries
cols <- as.vector(cols) # convert to a vector
cols <- cols[!is.na(cols)] # remove NA entries corresponding to diagonal
count <- 0 # panel number
my_panel <- function(x, y, ...) # panel function for colorizing groups
{ count <<- count + 1; points(x, y, pch = ".", col = cols[count]) }
pairs(U, panel = my_panel, gap = 0,
labels = as.expression( sapply(1:d, function(j) bquote(italic(U[.(j)]))) ))
## 3) Zenplot of a random path through all pairs, colorizing the respective group
## Define our own points_2d_grid() for colorizing the groups
my_points_2d_grid <- function(zargs, basecol, d.) {
r <- extract_2d(zargs) # extract information from zargs
x <- r$x
y <- r$y
xlim <- r$xlim
ylim <- r$ylim
num2d <- zargs$num/2
vars <- as.numeric(r$vlabs[num2d:(num2d+1)]) # two variables to be plotted
## Alternatively, we could have used ord[r$vars[num2d:(num2d+1)]] with
## the order 'ord' (see below) being passed to my_points_2d_grid()
col <- if(all(1 <= vars & vars <= d.[1])) { basecol[1] } else {
if(all(d.[1]+1 <= vars & vars <= d.[1]+d.[2])) { basecol[2] } else {
if(all(d.[1]+d.[2]+1 <= vars & vars <= d)) basecol[3] else "black"
}
} # determine the colors
vp <- vport(zargs$ispace, xlim = xlim, ylim = ylim, x = x, y = y) # viewport
pointsGrob(x = x[[1]], y = y[[1]], pch = 21, size = unit(0.02, units = "npc"),
name = "points_2d", gp = gpar(col = col), vp = vp)
}
## Plot a random permutation of columns via a zenplot
## Note: We set column labels here, as otherwise the labels can only
## show *indices* of the variables to be plotted, i.e., the column
## number in U[,ord], and not the original column number in U (which
## is what we want to see in order to see how our 'path' through
## the pairs of variables looks like).
colnames(U) <- 1:d
set.seed(1)
(ord <- sample(1:d, size = d)) # path; 1:d would walk parallel to the secondary diagonal
#> [1] 4 7 1 2 13 16 11 14 3 15 5 12 10 6 17 9 8
zenplot(U[,ord], plot1d = "layout", plot2d = "layout", pkg = "grid") # layout
zenplot(U[,ord], # has correct variable names as column names
pkg = "grid",
plot1d = function(zargs) arrow_1d_grid(zargs, col = "grey50"),
plot2d = function(zargs)
gTree(children = gList(
my_points_2d_grid(zargs, basecol = basecol, d. = d.),
rect_2d_grid(zargs, width = 1.05, height = 1.05,
col = "grey50", lty = 3),
label_2d_grid(zargs, loc = c(1.06, -0.03),
just = c("left", "top"), rot = 90, cex = 0.45,
fontface = "bold") )))
## => The points are colorized correctly (compare with the pairs plot).
# }
### Using ggplot2 ##############################################################
## Although not thoroughly tested, in principle ggplot2 can also be used via
## pkg = "grid" as follows.
# \donttest{
library(ggplot2)
## Define our own 2d plot
my_points_2d_ggplot <- function(zargs, extract2d = TRUE)
{
if(extract2d) {
r <- extract_2d(zargs) # extract results from zargs
df <- data.frame(r$x, r$y) # data frame
names(df) <- c("x", "y")
cols <- zargs$x[,"Species"]
} else {
ii <- plot_indices(zargs) # the indices of the variables to be plotted
irs <- zargs$x # iris data
df <- data.frame(x = irs[,ii[1]], y = irs[,ii[2]]) # data frame
cols <- irs[,"Species"]
}
num2d <- zargs$num/2 # plot number among all 2d plots
p <- ggplot() + geom_point(data = df, aes(x = x, y = y, colour = cols),
show.legend = num2d == 3) +
labs(x = "", y = "") # 2d plot
if(num2d == 3) p <- p + theme(legend.position = "bottom", # legend for last 2d plot
legend.title = element_blank())
ggplot_gtable(ggplot_build(p)) # 2d plot as grob
}
## Plotting
iris. <- iris
colnames(iris.) <- gsub("\\\\.", " ", x = colnames(iris)) # => nicer 1d labels
zenplot(iris., n2dplots = 3, plot2d = "my_points_2d_ggplot", pkg = "grid")
#> Error in zenplot(iris., n2dplots = 3, plot2d = "my_points_2d_ggplot", pkg = "grid"): Function provided as argument 'plot2d' does not exist.
zenplot(iris., n2dplots = 3,
plot2d = function(zargs) my_points_2d_ggplot(zargs, extract2d = FALSE),
pkg = "grid")
# }
### Providing your own data structure ##########################################
# \donttest{
## Danger zone: An example with a new data structure (here: a list of *lists*)
## Note: - In this case, we most likely need to provide both plot1d and plot2d
## (but not in this case here since arrow_1d_graphics() does not depend
## on the data structure)
## - Note that we still make use of zargs here.
## - Also note that the variables are not correctly aligned anymore:
## In the ggplot2 examples we guaranteed this by plot_indices(),
## but here we don't. This then still produces our layout but the
## x/y axis of adjacent plots might not be the same anymore. This is
## fine if only a certain order of the plots is of interest, but
## not a comparison between adjacent plots.
z <- list(list(1:5, 2:1, 1:3), list(1:5, 1:2))
zenplot(z, n2dplots = 4, plot1d = "arrow", last1d = FALSE,
plot2d = function(zargs, ...) {
r <- unlist(zargs$x, recursive = FALSE)
num2d <- zargs$num/2 # plot number among 2d plots
x <- r[[num2d]]
y <- r[[num2d + 1]]
if(length(x) < length(y)) x <- rep(x, length.out = length(y))
else if(length(y) < length(x)) y <- rep(y, length.out = length(x))
plot(x, y, type = "b", xlab = "", ylab = "")
}, ispace = c(0.2, 0.2, 0.1, 0.1))
# }
### Zenplots based on 3d lattice plots #########################################
# \donttest{
library(lattice)
library(grid)
library(gridExtra)
#>
#> Attaching package: ‘gridExtra’
#> The following object is masked from ‘package:BiocGenerics’:
#>
#> combine
## Build a list of cloud() plots (trellis objects)
## Note:
## - 'grid' problem: Without print(), the below zenplot() may fail (e.g.,
## in fresh R sessions) with: 'Error in UseMethod("depth") :
## no applicable method for 'depth' applied to an object of class "NULL"'
## - col = "black" inside scales is needed to make the ticks show
mycloud <- function(x, num) {
lim <- extendrange(0:1, f = 0.04)
print(cloud(x[, 3] ~ x[, 1] * x[, 2], xlim = lim, ylim = lim, zlim = lim,
xlab = substitute(U[i.], list(i. = num)),
ylab = substitute(U[i.], list(i. = num + 1)),
zlab = substitute(U[i.], list(i. = num + 2)),
zoom = 1, scales = list(arrows = FALSE, col = "black"),
col = "black",
par.settings = list(standard.theme(color = FALSE),
axis.line = list(col = "transparent"),
clip = list(panel = "off"))))
}
plst.3d <- lapply(1:4, function(i)
mycloud(x[,i:(i+2)], num = i)) # list of trellis objects
## Preparing the zenplot
num <- length(plst.3d)
ncols <- 2
turns <- c(rep("r", 2*(ncols-1)), "d", "d",
rep("l", 2*(ncols-1)), "d")
plot2d <- function(zargs) {
num2d <- (zargs$num+1)/2
vp <- vport(zargs$ispace, xlim = 0:1, ylim = 0:1)
grob(p = zargs$x[[num2d]], vp = vp, cl = "lattice") # convert trellis to grid object
## Note: For further plots, Work with
## gTree(children = gList(grob(zargs$x[[num2d]], vp = vp,
## cl = "lattice")))
}
## Zenplot
## Note: We use a list of *plots* here already (not data)
zenplot(plst.3d, turns = turns, n2dplots = num, pkg = "grid", first1d = FALSE,
last1d = FALSE, plot1d = "arrow_1d_grid", plot2d = plot2d)
# }