This should be fixed now int the latest devel version 1.1.15. I did find a related bug that prevented connecting lines of grouped track items to be plotted when zoomed in all the way between the two connected features. This should work now, too. Florian -- On 8/28/12 10:58 AM, "Hahne, Florian" <florian.hahne at="" novartis.com=""> wrote: >Hi Winston, >This obviously is a bug. I will have to take a closer look, but probably >won't have time before middle of September. It should be repaired with the >next Bioconductor release. >Thanks for reporting this, >Florian >-- > > > > > > >On 8/23/12 6:06 PM, "Winston Timp" <wtimp1 at="" jhmi.edu=""> wrote: > >>I have run into a different problem with the devel version of Gviz: >> >>If I try to plot a GeneRegionTrack derived from UCSC at a location which >>overlaps a gene, but none of its exons, it fails, complaining as shown >>below. If I extend the plot range to overlap with an exon, (AKA >>from=122426300), it works. >> >>Is there a workaround for this/am I making an obvious error? I assume >>that >>it is exploding because it expects at least one exon in the plotted >>region. >> Even if I set the collapseTranscripts flag, it still fails, probably >>because that step is after finding exons within region. >> >>traceback and sessionInfo below >> >>Thanks, >> >>Winston >> >>> library(Gviz) >>Loading required package: grid >>> genetrack=UcscTrack(track="RefSeq Genes", table="refGene", >>trackType="GeneRegionTrack",chromosome="chr5", genome="hg19", >>rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", >>transcript="name", strand="strand", name="RefSeq Genes", feature="name2", >>showId=T, from=122428653, to=122432628) >>> plotTracks(genetrack, from=122428653, to=122432628) >>Error in unit(rep(1, n), "strwidth", data = data) : >> 'x' and 'units' must have length > 0 >>> traceback() >>12: stop("'x' and 'units' must have length > 0") >>11: unit(rep(1, n), "strwidth", data = data) >>10: stringWidth(identifier(GdObject, add.space = TRUE)) >>9: is.unit(x) >>8: convertUnit(x, unitTo, "x", "dimension", "x", "dimension", valueOnly = >>valueOnly) >>7: convertWidth(stringWidth(identifier(GdObject, add.space = TRUE)), >> "native") >>6: .local(GdObject, ...) >>5: FUN(X[[1L]], ...) >>4: FUN(X[[1L]], ...) >>3: lapply(trackList, setStacks, from = ranges["from"], to = ranges["to"]) >>2: lapply(trackList, setStacks, from = ranges["from"], to = ranges["to"]) >>1: plotTracks(genetrack, from = 122428653, to = 122432628) >>> sessionInfo() >>R version 2.15.1 (2012-06-22) >>Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >>locale: >>[1] C/en_US.UTF-8/C/C/C/C >> >>attached base packages: >>[1] grid stats graphics grDevices utils datasets methods >>base >> >>other attached packages: >>[1] Gviz_1.1.12 >> >>loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.19.29 BSgenome_1.25.6 Biobase_2.17.6 >> [4] BiocGenerics_0.3.1 Biostrings_2.25.12 DBI_0.2-5 >> [7] GenomicFeatures_1.9.31 GenomicRanges_1.9.53 IRanges_1.15.40 >>[10] RColorBrewer_1.0-5 RCurl_1.91-1 RSQLite_0.11.1 >>[13] Rsamtools_1.9.28 XML_3.9-4 biomaRt_2.13.2 >>[16] bitops_1.0-4.1 lattice_0.20-6 rtracklayer_1.17.19 >>[19] stats4_2.15.1 tools_2.15.1 zlibbioc_1.3.0 >> >>-- >>Winston Timp >>(410)-417-8467 >>Postdoctoral Fellow >>Johns Hopkins Medicine >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at r-project.org >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor