[BioC] Gviz: plotTracks with GeneRegionTrack

Hahne, Florian florian.hahne at novartis.com
Tue Aug 28 10:58:49 CEST 2012

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,

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
>it is exploding because it expects at least one exon in the plotted
> Even if I set the collapseTranscripts flag, it still fails, probably
>because that step is after finding exons within region.
>traceback and sessionInfo below
>> 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 =
>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)
>[1] C/en_US.UTF-8/C/C/C/C
>attached base packages:
>[1] grid      stats     graphics  grDevices utils     datasets  methods
>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
>Postdoctoral Fellow
>Johns Hopkins Medicine
>	[[alternative HTML version deleted]]
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