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setMethod(
f = "plotQuality",
signature = "FastqFileList",
definition = function(x, ..., col=rainbow(length(x)))
{
quals <- lapply(x, function(x) {
fq <- quality(readFastq(x))
wd <- unique(width(fq))
if (1L != length(wd)) {
minwd <- min(wd)
message(paste("reducing width to trailing ", minwd,
"\n path: ", path(x)))
fq <- narrow(fq, start=1, end=minwd)
}
colMeans(as(fq, "matrix"))
})
wd <- max(sapply(quals, length))
min <- min(sapply(quals, min))
max <- max(sapply(quals, max))
plot(quals[[1]], xlim=c(1, wd), ylim=c(min, max), type="b",
..., xlab="Cycle", ylab="Quality", col=col[1])
for (i in 1 + seq_along(quals[-1]))
lines(quals[[i]], type="l", col=col[i])
invisible()
})
setMethod(
f = "barplot",
signature = signature(height="FastqFileList"),
definition = function(height,...) {
x <- lapply(height,function(x) length(readFastq(x)))
barplot(unlist(x),...)
}
)
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