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## This is totally wrong and needs updating to match the new
## code in permute...
`permuplot` <- function(n, control = how(),
col = par("col"),
hcol = "red",
shade = "lightgrey",
xlim=NULL, ylim=NULL,
inset = 0.1,
main=NULL, sub=NULL,
ann = par("ann"),
cex = par("cex"),
...) {
## This should just bail with an message
message("permuplot does not work with the new permutation designs.\nNo plot will be generated!")
invisible()
xy.series <- function(n) {
angle <- seq(0, 2*pi, length = n+1)[-(n+1)]
x <- rev(cos(angle))
y <- rev(sin(angle))
xy <- xy.coords(x, y)
return(xy)
}
xy.free <- function(n) {
x <- runif(n)
y <- runif(n)
xy <- xy.coords(x, y)
return(xy)
}
xy.grid <- function(ncol, nrow) {
x <- rep(seq_len(ncol), each = nrow)
y <- rev(rep(seq_len(nrow), times = ncol))
xy <- xy.coords(x, y)
return(xy)
}
axis.limits <- function(vals, inset) {
lim <- range(vals[is.finite(vals)])
lim.range <- lim[2] - lim[1]
res <- c(lim[1] - (lim.range * inset),
lim[2] + (lim.range * inset))
return(res)
}
## currently doesn't support restricted permutations of strata themselves
if(control$permute.strata && control$type != "free")
stop("Restricted permutations of strata currently not supported")
## check that n and length of strata are equal
if( use.strata <- !is.null(control$strata) ) {
tab <- table(control$strata)
if(!identical(as.integer(sum(tab)), as.integer(n)))
stop("'n' and length of 'strata' don't match.")
}
## check the control design
control <- check(n, control = control)$control
if(use.strata) {
n.grp <- length(tab)
opar <- par(no.readonly=TRUE, mar=c(2,2,2,1)+0.1,
mfrow = n2mfrow(n.grp),
oma=c(2.1,0,3.1,0))
on.exit(par(opar))
## if permuting strata, only need to draw the sub-plots
## in a different order
if(control$permute.strata) {
## expand shade, col
if(identical(length(col), 1))
col <- rep(col, n.grp)
if(identical(length(shade), 1))
shade <- rep(shade, n.grp)
ord <- sample(names(tab))
if(is.null(xlim))
xlim <- c(0,1)
if(is.null(ylim))
ylim <- c(0,1)
xy <- xy.coords(0.5, 0.5)
string <- paste("Stratum:\n", ord)
names(string) <- ord
strh <- max(strheight(string, cex = cex))
strw <- max(strwidth(string, cex = cex))
box.coords <- xy.coords(rep(c(0.5-strw, 0.5+strw), each = 2),
c(0.5-strh, 0.5+strh,
0.5+strh, 0.5-strh))
for(i in ord) {
plot.new()
plot.window(xlim, ylim, asp = 1, ...)
polygon(box.coords, col = shade, border = hcol, ...)
text(xy$x, xy$y, labels = string[i],
col = col, cex = cex, ...)
box()
#if(ann) {
# title(main = paste("Original order:",
# which(ord == i)))
#}
}
} else {
## if free and constant, only need one set of random coords
xy <- if(control$constant && control$type == "free") {
## needs to be a list for the main loop below
xy <- xy.free(unique(tab))
res <- vector("list", length = length(tab))
for(i in seq_along(res)) {
res[[i]] <- xy
}
res
} else {
switch(control$type,
free = lapply(tab, xy.free),
series = lapply(tab, xy.series),
grid = lapply(tab, function(x) {
xy.grid(control$ncol, control$nrow)
}),
stop("Unsupport permutation 'type'"))
}
perms <- shuffle(n, control = control)
perms <- tapply(perms, control$strata, function(x) x)
if(is.null(main))
main <- paste("Stratum:", names(tab))
for(i in seq_along(xy)) {
if(is.null(xlim))
xlim <- axis.limits(xy[[i]]$x, inset)
if(is.null(ylim))
ylim <- axis.limits(xy[[i]]$y, inset)
plot.new()
plot.window(xlim, ylim, asp = 1, ...)
cols <- switch(control$type,
free = rep(col, tab[i]),
series = c(hcol, rep(col, tab[i]-1)),
grid = {cols <- rep(col, tab[i])
cols[which.min(perms[[i]])] <-
hcol
cols})
text(xy[[i]]$x, xy[[i]]$y, labels = perms[[i]],
col = cols, ...)
if(ann) {
title(main = main[i], ...)
title(sub = paste("n in stratum:", tab[i]),
line = 0.5, ...)
}
box()
}
}
if(ann) {
sub <- paste(paste("n: ", n, ";", sep = ""),
paste("mirror: ", control$mirror, ";",
sep = ""),
paste("constant: ", control$constant, ";",
sep = ""),
sep = " ")
if(control$type == "grid")
sub <- paste(sub, paste("ncol: ",
control$ncol, ";",
sep = ""),
paste("nrow: ", control$nrow, ";",
sep = ""),
sep = " ")
title(main = paste("Permutation type:", control$type),
outer = TRUE, cex.main = 1.75, ...)
title(sub = sub, outer = TRUE, line = 0.5,
cex.sub = 1, ...)
}
} else {
xy <- switch(control$type,
free = xy.free(n),
series = xy.series(n),
grid = xy.grid(control$ncol, control$nrow),
stop("Unsupport permutation 'type'"))
if(is.null(xlim)) {
xlim <- axis.limits(xy$x, inset)
}
if(is.null(ylim)) {
ylim <- axis.limits(xy$y, inset)
}
opar <- par(no.readonly=TRUE, mar=c(2,1,3,1)+0.1)
on.exit(par(opar))
if(is.null(main))
main <- paste("Permutation type:", control$type)
if(is.null(sub))
sub <- paste(paste("n: ", n, ";", sep = ""),
paste("mirror: ", control$mirror, ";",
sep = ""),
sep = " ")
plot.new()
plot.window(xlim, ylim, asp = 1, ...)
labs <- shuffle(n, control=control)
cols <- switch(control$type,
free = rep(col, n),
series = c(hcol, rep(col, n-1)),
grid = {cols <- rep(col, n)
cols[which.min(labs)] <- hcol
cols})
text(xy$x, xy$y, labels = labs,
col = cols, ...)
if(ann) {
title(main = main, ...)
title(sub = sub, line = 0.5, ...)
}
box()
}
invisible()
}
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