`plot.timetrack` <- function(x, choices = 1:2,
display = c("wa","lc"),
order,
type = c("p", "n"),
ptype = c("l", "p", "o", "b", "n"),
pch = c(1,2),
col = c("black","red"),
lty = "solid", lwd = 1,
xlim = NULL, ylim = NULL, ...) {
ptype <- match.arg(ptype)
type <- match.arg(type)
display <- match.arg(display)
scrs <- scores(x$ord, choices = choices, scaling = x$scaling,
display = display, ...)
pass <- fitted(x, type = "passive", choices = choices)
if (is.null(xlim)) {
xlim <- range(scrs[,1], pass[,1])
}
if (is.null(ylim)) {
ylim <- range(scrs[,2], pass[,2])
}
plt <- plot(x$ord, choices = choices, scaling = x$scaling,
type = "n", display = display, ...,
ylim = ylim, xlim = xlim)
if (isTRUE(all.equal(type, "p"))) {
points(scrs, pch = pch[1], col = col[1], ...)
}
if(!missing(order)) {
if(length(order) != NROW(pass))
stop("'length(order)' not equal to number of passive samples.")
pass[order, ]
}
if(ptype %in% c("l", "o", "b")) {
lines(pass, pch = pch[2], col = col[2],
lty = lty, lwd = lwd, type = ptype, ...)
} else if (isTRUE(all.equal(ptype, "p"))) {
points(pass, pch = pch[2], col = col[2], ...)
}
invisible(x$ord)
}
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