# R/polys.R In StatDA: Statistical Analysis for Environmental Data

```polys <-
function (x, scale = TRUE, labels = dimnames(x)[[1]],
locations = NULL, nrow = NULL, ncol = NULL, key.loc = NULL,
key.labels = dimnames(x)[[2]], key.xpd = TRUE, xlim = NULL,
ylim = NULL, flip.labels = NULL, factx=1,facty=1,
col.stars = NA, axes = FALSE, frame.plot = axes, main = NULL,
sub = NULL, xlab = "", ylab = "", cex = 0.8, lwd = 1.1,
lty = par("lty"), xpd = FALSE, mar = pmin(par("mar"), 1.1 +
c(2 * axes + (xlab != ""), 2 * axes + (ylab != ""), 1,
0)), add = FALSE, plot = TRUE, ...)
{
# draw polygons as multivariate graphics
#
if (is.data.frame(x))
x <- data.matrix(x)
else if (!is.matrix(x))
stop("'x' must be a matrix or a data frame")
if (!is.numeric(x))
stop("data in 'x' must be numeric")
n.loc <- nrow(x)
n.seg <- ncol(x)
if (is.null(locations)) {
if (is.null(nrow))
nrow <- ceiling(if (!is.numeric(ncol)) sqrt(n.loc) else n.loc/ncol)
if (is.null(ncol))
ncol <- ceiling(n.loc/nrow)
if (nrow * ncol < n.loc)
stop("nrow * ncol <  number of observations")
ff <- if (!is.null(labels)) 2.3
else 2.1
locations <- expand.grid(ff * 1:ncol, ff * nrow:1)[1:n.loc, ]
if (!is.null(labels) && (missing(flip.labels) || !is.logical(flip.labels)))
flip.labels <- ncol * mean(nchar(labels, type = "c")) > 30
}
else {
if (is.numeric(locations) && length(locations) == 2) {
locations <- cbind(rep.int(locations[1], n.loc),
rep.int(locations[2], n.loc))
if (!missing(labels) && n.loc > 1)
warning("labels do not make sense for a single location")
else labels <- NULL
}
else {
if (is.data.frame(locations))
locations <- data.matrix(locations)
if (!is.matrix(locations) || ncol(locations) != 2)
stop("'locations' must be a 2-column matrix.")
if (n.loc != nrow(locations))
stop("number of rows of 'locations' and 'x' must be equal.")
}
if (missing(flip.labels) || !is.logical(flip.labels))
flip.labels <- FALSE
}
xloc <- locations[, 1]
yloc <- locations[, 2]
if (scale) {
x <- apply(x, 2, function(x) (x - min(x, na.rm = TRUE))/diff(range(x,
na.rm = TRUE)))
}
x[is.na(x)] <- 0
mx <- max(x <- x * factx)
if (is.null(xlim))
xlim <- range(xloc) + c(-mx, mx)
if (is.null(ylim))
ylim <- range(yloc) + c(-mx, mx)
op <- par(mar = mar, xpd = xpd)
on.exit(par(op))
plot(0, type = "n", ..., xlim = xlim, ylim = ylim, main = main,
sub = sub, xlab = xlab, ylab = ylab, asp = 1, axes = axes)
if (!plot)
return()
s.x <- seq(-factx*n.seg/2,factx*n.seg/2, length=n.seg)

for (i in 1:n.loc) {
xco <- s.x+xloc[i]
yco <- yloc[i]+x[i,]*facty
lines(xco,yco,lwd=lwd, ...)
lines(c(xco[1],xco[length(xco)]),c(yloc[i],yloc[i]),lwd=0.7)
}
if (!is.null(labels)) {
y.off <- mx
if (flip.labels)
y.off <- y.off + cex * par("cxy")[2] * ((1:n.loc)%%2 - 0.4)
text(xloc, yloc - y.off, labels, cex = cex, adj = c(0.5, 1))
}
if (!is.null(key.loc)) {
par(xpd = key.xpd)

xco <- 2.2*s.x + key.loc[1]
yco <- key.loc[2] +x[3,]*facty*2.2
lines(xco,yco,lwd=lwd, ...)
#lines(c(xco[1],xco[length(xco)]),c(key.loc[1],key.loc[2]))
segments(xco[1],key.loc[2],xco[length(xco)],key.loc[2],lwd=0.7)

label.x <- 2.2*s.x + key.loc[1]
label.y <- key.loc[2] - y.off*1.5
text(label.x, label.y, labels = key.labels, cex = cex)
}
if (frame.plot)
box(...)
invisible(locations)
}
```

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StatDA documentation built on March 13, 2020, 2:42 a.m.