Nothing
plot.haploAccum <-
function(x, add = FALSE, ci = 2, ci.type = c("bar","line","polygon"),
col = par("fg"), ci.col = col, ci.lty = 1, xlab,
ylab = "Haplotypes", ylim, main = paste(x$method, "method of haplotype accumulation", sep=" "), ...)
{
xaxvar <- x[["sequences"]]
if (missing(xlab)) xlab <- "Sequences"
ci.type <- match.arg(ci.type)
if (!add) {
if (missing(ylim))
ylim <- c(1, max(x$n.haplotypes, x$n.haplotypes + ci*x$sd))
plot(xaxvar, x$n.haplotypes, xlab=xlab, ylab=ylab, ylim=ylim,
type="n", main = main, ...)
}
if (!is.null(x$sd) && ci)
switch(ci.type,
bar = segments(xaxvar, x$n.haplotypes - ci*x$sd, xaxvar,
x$n.haplotypes + ci*x$sd, col=ci.col, lty=ci.lty, ...),
line = matlines(xaxvar, x$n.haplotypes + t(rbind(-ci,ci) %*% x$sd),
col=ci.col, lty=ci.lty, ...),
polygon = polygon(c(xaxvar, rev(xaxvar)),
c(x$n.haplotypes - ci*x$sd, rev(x$n.haplotypes + ci*x$sd)), col=ci.col,
lty=ci.lty, main = main, ...)
)
lines(xaxvar, x$n.haplotypes,col=col, ...)
invisible()
}
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