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plotladder <- function(abifdata, chanel, calibr, allele.names = "identifiler", npeak = NULL, ...){
old.par <- par(no.readonly = TRUE)
on.exit(par(old.par))
data(list = allele.names,envir=environment())
tmp <- get(allele.names)[chanel]
if(is.null(npeak)) npeak <- length(unlist(tmp))
x <- calibr(peakabif(abifdata, chanel, npeak = npeak, ...)$maxis)
n <- length(x)
par(mfrow = c(1,1), mar = c(5,0,4,0)+0.1)
labels <- unlist(tmp)
col <- rep("black", n)
col[grep("\\.", labels)] <- "red"
y <- rep(1.1, n)
y[grep("\\.", labels)] <- 1.3
dyn <- abifdata$Data[[paste("DyeN", chanel, sep = ".")]]
main <- paste(abifdata$Data[["RunN.1"]], "\nwith fluorochrome", dyn)
main <- paste("Observed allelic ladder for", main)
plot(x, y, type = "h", ylim = c(0,1.5), col = col, yaxt = "n", ylab = "",
xlab = "Observed size [bp]", main = main)
text(x, y + 0.1, labels, srt = 90, col = col)
nlocus <- unlist(lapply(tmp, length))
nallploc <- unlist(lapply(tmp,function(x) sapply(x,length)))
loc.pos <- c(1, cumsum(nallploc[1:(nlocus-1)])+1)
locnames <- unlist(lapply(tmp, names))
rect(x[loc.pos], rep(0.4, nlocus), x[cumsum(nallploc)], rep(0.6, nlocus), col = "lightblue")
text(x[loc.pos], 0.5, locnames, pos = 4)
invisible(x)
}
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