Nothing
`ordiplot` <-
function (ord, choices = c(1, 2), type = "points", display, xlim,
ylim, cex = 0.7, ...)
{
## local functions to absorb non-par arguments of plot.default
localPoints <- function(..., log, frame.plot, panel.first,
panel.last, axes) points(...)
localText <- function(..., log, frame.plot, panel.first,
panel.last, axes) text(...)
if (inherits(ord, "decorana") || inherits(ord, "cca")) {
if (missing(display))
out <- plot(ord, choices = choices, type = type, xlim = xlim,
ylim = ylim, cex = cex, ...)
else out <- plot(ord, choices = choices, type = type, display = display,
xlim = xlim, ylim = ylim, cex = cex, ...)
}
else {
type <- match.arg(type, c("points", "text", "none"))
## Matching displays could be done better (see
## ordipointlabel), but this may not be yet broken, so...
dplays <- c("sites", "species")
if (missing(display))
display <- dplays
else
display <- match.arg(display, dplays, several.ok = TRUE)
X <- Y <- NULL
if ("sites" %in% display)
X <- scores(ord, choices = choices, display = "sites")
if ("species" %in% display) {
op <- options(show.error.messages = FALSE)
Y <- try(scores(ord, choices = choices, display = "species"))
options(op)
if (inherits(Y, "try-error")) {
message("species scores not available")
Y <- NULL
}
else if (!is.null(X) && NROW(X) == NROW(Y) &&
isTRUE(all.equal.numeric(X, Y,
check.attributes = FALSE))) {
Y <- NULL
message("species scores not available")
}
}
if (is.null(X) && is.null(Y))
stop("no scores found: nothing to plot")
## Use linestack and exit if there is only one dimension
if (NCOL(X) == 1 && NCOL(Y) == 1) {
pl <- linestack(X, ylim = range(c(X,Y), na.rm=TRUE), cex = cex, ...)
if (!is.null(Y))
linestack(Y, side = "left", add = TRUE, cex = cex, ...)
return(invisible(pl))
}
tmp <- apply(rbind(X, Y), 2, range, na.rm=TRUE)
if (missing(xlim))
xlim <- tmp[, 1]
if (missing(ylim))
ylim <- tmp[, 2]
plot(tmp, xlim = xlim, ylim = ylim, asp = 1, type = "n",
...)
if (type == "points") {
if (!is.null(X))
localPoints(X, pch = 1, col = 1, cex = cex, ...)
if (!is.null(Y))
localPoints(Y, pch = "+", col = "red", cex = cex, ...)
}
if (type == "text") {
if (!is.null(X)) {
labs <- rownames(X)
if (is.null(labs)) {
warning("type='t', but no names available: using x1...")
labs <- paste0("x", as.character(seq_len(nrow(X))))
}
localText(X, labels = labs, col = 1, cex = cex, ...)
}
if (!is.null(Y)) {
labs <- rownames(Y)
if (is.null(labs)) {
warning("type='t', but no names available: using y1...")
labs <- paste0("y", as.character(seq_len(nrow(Y))))
}
localText(Y, labels = labs, col = "red", cex = cex, ...)
}
}
out <- list(sites = X, species = Y)
}
class(out) <- "ordiplot"
invisible(out)
}
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