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plotabif <- function(abifdata,
chanel = 1,
tmin = 1/tscale,
tmax = abifdata$Data[["SCAN.1"]]/tscale,
tscale = 1000,
yscale = 1000, type = "l", las = 1,
xlab = paste("Time", tscale, sep = "/"),
ylab = paste("RFU", yscale, sep = "/"),
irange = (tmin*tscale):(tmax*tscale),
x = irange/tscale,
xlim = c(tmin, tmax),
chanel.names = c(1:4,105),
DATA = paste("DATA", chanel.names[chanel], sep = "."),
y = abifdata$Data[[DATA]][irange]/yscale,
ylim = c(min(y), max(y)),
dyn = abifdata$Data[[paste("DyeN", chanel, sep = ".")]],
main = paste(deparse(substitute(abifdata)), chanel, dyn, sep = " ; "),
calibr = NULL,
ladder.bp = NULL,
allele.names = "identifiler",
ladder.lab = TRUE,
...){
old.par <- par(no.readonly = TRUE)
on.exit(par(old.par))
if(is.null(calibr)){
plot(x, y, type = type, las = las,
xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim, main = main, ...)
} else {
x <- calibr(irange)
xlim <- range(x)
plot(x, y, type = type, las = las,
xlab = "Size [bp]", ylab = ylab, xlim = xlim, ylim = ylim, main = main, ...)
tps <- pretty(irange)
par(cex=0.5)
axis(1, at = calibr(tps), tps/tscale, line = 0.4, col = grey(0.5))
par(cex=1)
if(!is.null(ladder.bp)){ # Allelic ladder add
data(list = allele.names,envir=environment())
tmp <- get(allele.names)[chanel]
n <- length(ladder.bp)
labels <- unlist(tmp)
col <- rep("black", n)
col[grep("\\.", labels)] <- "red"
abline(v = ladder.bp, col = col)
if(ladder.lab){
text(ladder.bp, y = par("usr")[4], labels, xpd = NA,
pos = 3, srt = 45, col = col, cex = 0.8)
}
}
}
locpar <- par(no.readonly = TRUE)
invisible(locpar)
}
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