[BioC] Gviz: plotTracks with GeneRegionTrack

Hahne, Florian florian.hahne at novartis.com
Fri Sep 7 08:47:59 CEST 2012

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.

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,
>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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>>Bioconductor at r-project.org
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