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### $Id: plothier.q 6800 2014-09-04 08:29:53Z maechler $
pltree <- function(x, ...) UseMethod("pltree")
## note: pltree() can have an 'xlab' in "..." (plot.hclust has an explicit one)
pltree.twins <- function(x, main = paste("Dendrogram of ", deparse(x$call)),
labels = NULL, ylab = "Height", ...)
{
plot(as.hclust(x), labels = labels,
##- if(is.null(labels) && length(x$order.lab) != 0)
##- labels <- x$order.lab[sort.list(x$order)]
##-
##- ## calling plot.hclust() via generic :
##- plot(structure(list(merge = x$merge, order = x$order,
##- height = sort(x$height), labels = labels,
##- call = x$call, method = x$method),
##- class = "hclust"),
main = main, ylab = ylab, ...)
}
bannerplot <-
function(x, w = rev(x$height), fromLeft = TRUE, main=NULL, sub=NULL,
xlab = "Height", adj = 0, col = c(2, 0), border = 0,
axes = TRUE, frame.plot = axes, rev.xax = !fromLeft, xax.pretty = TRUE,
labels = NULL, nmax.lab = 35, max.strlen = 5,
yax.do = axes && length(x$order) <= nmax.lab,
yaxRight = fromLeft, y.mar = 2.4 + max.strlen / 2.5, ...)
{
m <- max(w)
if(axes) {
if(xax.pretty) {
at.vals <- if(!is.logical(xax.pretty))
pretty(c(0,w), n = xax.pretty) else pretty(c(0,w))
n <- length(at.vals <- at.vals[at.vals <= m])
if(at.vals[n] * 1.01 < m) {
lab.vals <- c(at.vals, signif(m, 3))
at.vals <- c(at.vals, m)
} else lab.vals <- at.vals
} else { # old default for plot.agnes() and plot.diana()
ss <- seq(0, floor(m), length = 11)# => intervals = 1/10 {total}
at.vals <- c(ss, m)
lab.vals <- round(at.vals, 2)
}
}
if(fromLeft) {
w <- rbind(w, m - w)
if(missing(col)) col <- rev(col)
} else { ## from Right
w <- rbind(m - w, w)
if(axes && rev.xax) {
at.vals <- m - rev(at.vals)## == c(0, ss + m - floor(m))
lab.vals <- rev(lab.vals)
}
}
if(yax.do) {
ax <- if(yaxRight)
list(side = 4, pos = m)
else list(side = 2, pos = 0)
if((pm <- par("mar"))[ax$side] < y.mar) {
## need space besides y axis for labeling
pm[ax$side] <- y.mar
op <- par(mar = pm)
on.exit(par(op))
}
}
barplot(w, xlab = xlab, horiz = TRUE, space = 0, axes = FALSE,
col = col, border = border, mgp = c(2.5, 1, 0), ...)
if(frame.plot && (border == 0 || border == par("bg")))
rect(0, 0, m, ncol(w))
title(main = main, sub = sub, adj = adj)
if(axes) {
axis(1, at = at.vals, labels = lab.vals, ...)
if(yax.do) {
if(is.null(labels))
labels <- rev(if (length(x$order.lab) != 0)
substring(x$order.lab, 1,max.strlen) else x$order)
axis(ax$side, at = 0:(length(x$order) - 1), las = 1,
labels = labels, pos = ax$pos, mgp = c(3, 1.25, 0), ...)
}
}
invisible()
}
## plot.diana() [further down] & plot.agnes() are almost identical;
## -- made bannerplot() a stand-alone function
## --> maybe *merge* these two into one plot.twins()
plot.agnes <-
function(x, ask = FALSE, which.plots = NULL, main = NULL,
sub = paste("Agglomerative Coefficient = ", round(x$ac, digits = 2)),
adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)
{
if(is.null(main)) {
cl <- paste(strwrap(deparse(x$call, 150)[1], width = 60, exdent = 7),
collapse="\n")
## Different default for banner & pltree:
main1 <- paste("Banner of ", cl)
main2 <- paste("Dendrogram of ", cl)
}
else { # same title for both
main1 <- main2 <- main
}
if(is.null(which.plots) && !ask)
which.plots <- 1:2
if(ask && is.null(which.plots)) { ## Use 'menu' ..
tmenu <- paste("plot ", ## choices :
c("All", "Banner", "Clustering Tree"))
do.all <- FALSE
repeat {
if(!do.all)
pick <- menu(tmenu, title =
"\nMake a plot selection (or 0 to exit):\n") + 1
switch(pick,
return(invisible()), # 0 -> exit loop
do.all <- TRUE,# 1 : All
bannerplot(x, fromLeft = TRUE,
main = main1, sub = sub, adj = adj,
xax.pretty = 10,
nmax.lab= nmax.lab, max.strlen= max.strlen, ...),
pltree (x, main = main2, sub = sub, ...) # 3
)
if(do.all) { pick <- pick + 1; do.all <- pick <= length(tmenu) + 1}
}
}
else {
ask <- prod(par("mfcol")) < length(which.plots) && dev.interactive()
if(ask) {
op <- par(ask = TRUE)
on.exit(par(op))
}
for(i in which.plots)
switch(i,
bannerplot(x, fromLeft = TRUE,
main = main1, sub = sub, adj = adj,
xax.pretty = 10,
nmax.lab = nmax.lab, max.strlen = max.strlen, ...),
pltree (x, main = main2, sub = sub, ...)
)
}
invisible()
}
plot.diana <-
function(x, ask = FALSE, which.plots = NULL, main = NULL,
sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),
adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)
{
if(is.null(main)) {
cl <- paste(strwrap(deparse(x$call, 150)[1], width = 60, exdent = 7),
collapse="\n")
## Different default for banner & pltree:
main1 <- paste("Banner of ", cl)
main2 <- paste("Dendrogram of ", cl)
}
else { # same title for both
main1 <- main2 <- main
}
if(is.null(which.plots) && !ask)
which.plots <- 1:2
if(ask && is.null(which.plots)) { ## Use 'menu' ..
tmenu <- paste("plot ", ## choices :
c("All", "Banner", "Clustering Tree"))
do.all <- FALSE
repeat {
if(!do.all)
pick <- menu(tmenu, title =
"\nMake a plot selection (or 0 to exit):\n") + 1
switch(pick,
return(invisible()), # 0 -> exit loop
do.all <- TRUE,# 1 : All
bannerplot(x, fromLeft = FALSE,
main = main1, sub = sub, adj = adj,
xax.pretty = 10,
nmax.lab= nmax.lab, max.strlen= max.strlen, ...),
pltree (x, main = main2, sub = sub, ...)
)
if(do.all) { pick <- pick + 1; do.all <- pick <= length(tmenu) + 1}
}
}
else {
ask <- prod(par("mfcol")) < length(which.plots) && dev.interactive()
if(ask) {
op <- par(ask = TRUE)
on.exit(par(op))
}
for(i in which.plots)
switch(i,
bannerplot(x, fromLeft = FALSE, main = main1, sub = sub,
adj = adj, xax.pretty = 10,
nmax.lab = nmax.lab, max.strlen = max.strlen, ...),# 1
pltree (x, main = main2, sub = sub, ...) # i = 2
)
}
invisible()
}
plot.mona <- function(x, main = paste("Banner of ", deparse(x$call)),
sub = NULL, xlab = "Separation step",
col = c(2,0), axes = TRUE, adj = 0,
nmax.lab = 35, max.strlen = 5, ...)
{
w <- rev(x$step)
m <- max(w)
if(any(i0 <- w == 0))
w[i0] <- m <- m+1
bannerplot(x[c("order","order.lab")], w = w, fromLeft = TRUE,
yaxRight = FALSE, col = col, main = main, sub = sub, xlab = xlab,
adj= adj, axes= axes, nmax.lab= nmax.lab, max.strlen= max.strlen,
xax.pretty = m+1, ...)
names <- paste(" ", rev(x$variable))
is.na(names) <- i0
text(w, 1:length(names) - 0.5, names, adj = 0, col = col[1], ...)
}
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