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]]

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