Hello Deepayan, Thanks for giving me a hand with xyplot.
The output of str(nread.islands) is > nread.islands <- as(gdapply(E1, islandReadSummary), "data.frame") > str(nread.islands) 'data.frame': 4886 obs. of 4 variables: $ nread : num 1 2 3 4 5 6 7 8 9 10 ... $ count : num 80871 12722 2548 666 176 ... $ chromosome: Factor w/ 21 levels "chr1.fa","chr10.fa",..: 1 1 1 1 1 1 1 1 1 1 ... $ sample : Factor w/ 4 levels "C1","C2","T1",..: 1 1 1 1 1 1 1 1 1 1 ... > Aha! I see what you mean. Instead of using chromosome == "chr19" I should be using chromosome == "chr19.fa" Now I am logged in remotely to my work computer. Bad connection. I'll try it tomorrow and let you know if it works. Thank you. Ivan ----- Original Message ---- From: Deepayan Sarkar <[email protected]> To: [email protected] Cc: [email protected] Sent: Tuesday, 28 April, 2009 19:01:16 Subject: Re: [Bioc-sig-seq] Error while trying to xyplot. Perhaps a lattice problem. On Tue, Apr 28, 2009 at 9:58 AM, <[email protected]> wrote: > > Hello everybody, > > I am working with the yet unreleased package chipseq. > > There is a very nice xyplot that I am trying to reproduce from the > > http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/ChipSeqWorkflow.pdf > > However, R complains saying > > "Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel, : > need at least one panel" > > What am I doing? This > >> class(E1) > [1] "GenomeDataList" > attr(,"package") > [1] "BSgenome" >> names(E1) > [1] "C1" "C2" "T1" "T2" >> islandReadSummary <- function(x) > + { > + g <- extendReads(x, seqLen = 200) > + s <- slice(coverage(g, 1, max(end(g))), lower = 1) > + tab <- table(viewSums(s) / 200) > + ans <- data.frame(nread = as.numeric(names(tab)), count = as.numeric(tab)) > + ans > + } >> nread.islands <- as(gdApply(E1, islandReadSummary), "data.frame") > There were 50 or more warnings (use warnings() to see the first 50) Could you share the output of str(nread.islands) ? >> xyplot(log(count) ~ nread | sample, > + nread.islands, > + subset = (chromosome == "chr19" & nread <= 40), > + layout = c(1, 4), pch = 16, type = c("p", "g")) > Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel, : > need at least one panel >> > > Can anybody shed some light? > > Clarification: the warning "There were 50 or more warnings (use warnings() to > see the first 50)" comes from IRanges. chipseq is using the slightly older > start/end convention rather than the newer shift/step convention. > Actually, that's happening inside your 'islandReadSummary' function, where s <- slice(coverage(g, 1, max(end(g))), lower = 1) should now be s <- slice(coverage(g), lower = 1) -Deepayan > Thank you, > > Ivan > > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
