Dear all,

I'm new to ggbio and can't seem to find an solution. I have a GRanges object gr containing ChIP-seq  data (on all chromosomes, imported with rtracklayer0, and want to plot just a detail on one chromosome, using

autoplot(gr, geom="line", aes(y=score), zoom.region=GRanges(seqnames="chrI", IRanges(10000, 11000)))

i.e. gr is the GRanges object, and I want to see the peaks on chrI, from 10 to 11 kb.

Instead the plotter takes ages and produces peaks for *all* the chromosomes (and which appear to be wrong anyway). Using xlim=, or which=  (instead of zoom.region) doesn't solve it.

If I do it as follows:

   gr2 <- gr[seqnames(gr)=="chrI" & start(gr)> 10000 & end(gr)<11000]
   autoplot(gr2, geom="line", aes(y=score))

it works, but that defeats the whole purpose of xlim (or the similar other arguments)

What am I doing wrong? Cheers,

Philip

I don't see a 'zoom.region' argument for any of the autoplot methods, so it's not surprising that it doesn't do what you expect. In addition, I don't believe there is a 'which' nor an 'xlim' argument for a GRanges object:

 ## S4 method for signature 'GRanges'
     autoplot(object, ..., chr, xlab, ylab, main, truncate.gaps = FALSE,
                      truncate.fun = NULL, ratio = 0.0025, space.skip = 0.1,
                      legend = TRUE, geom = NULL, stat = NULL,
                      chr.weight = NULL,
                      coord = c("default", "genome", "truncate_gaps"),
                      layout = c("linear", "karyogram", "circle"))

There is an xlim function that will modify your plot,

gr <- GRanges("chr2", IRanges(1e5,1e6))

autoplot(gr) + xlim(GRanges("chr2", IRanges(1e5,3e5)))

But that just seems silly. Why wouldn't you just modify your GRanges, which is like, super easy to do?