[BioC] Gviz error with collapseTranscripts=TRUE

[Stephanie M. Gogarten]

Hi,

I'm getting the error below with Gviz when I create a GeneRegionTrack 
with collapseTranscipts=TRUE.  The same data plots fine with 
collapseTranscripts=FALSE.  Plotting other transcripts with 
collapseTranscripts=TRUE also works - it seems to be something with this 
particular set of ranges.

gene.db <- select(Homo.sapiens, keys=c("CHRNA9", "UGT2B10", "UGT2A1"),
                   columns=c("GENEID", "GENENAME"), keytype="SYMBOL")
gene.tx <- transcripts(Homo.sapiens,
                        vals=list("gene_id"=gene.db$GENEID),
                        columns=c("GENEID", "TXNAME", "SYMBOL"))
names(mcols(gene.tx)) <- c("gene", "transcript", "symbol")

itrack <- IdeogramTrack(genome="hg19", chromosome="chr4")
gtrack <- GenomeAxisTrack()
genetrack <- GeneRegionTrack(gene.tx,
                              genome="hg19", chromosome="chr4",
                              showId=TRUE, collapseTranscripts=TRUE)
plotTracks(list(itrack, gtrack, genetrack))
Error in mk_elementMetadataReplacementValue(x, value) :
   3 rows in value to replace 4 rows

thanks,
Stephanie


sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] Homo.sapiens_1.1.1
  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
  [3] org.Hs.eg.db_2.9.0
  [4] GO.db_2.9.0
  [5] RSQLite_0.11.4
  [6] DBI_0.2-7
  [7] OrganismDbi_1.3.9
  [8] GenomicFeatures_1.13.14
  [9] GenomicRanges_1.13.16
[10] XVector_0.1.0
[11] IRanges_1.19.10
[12] AnnotationDbi_1.23.15
[13] Biobase_2.21.3
[14] BiocGenerics_0.7.2
[15] Gviz_1.5.4

loaded via a namespace (and not attached):
  [1] biomaRt_2.17.1     Biostrings_2.29.4  biovizBase_1.9.2 
bitops_1.0-5
  [5] BSgenome_1.29.0    cluster_1.14.4     colorspace_1.2-2 
dichromat_2.0-0
  [9] graph_1.39.2       Hmisc_3.10-1.1     labeling_0.1 
lattice_0.20-15
[13] munsell_0.4        plyr_1.8           RBGL_1.37.2 
RColorBrewer_1.0-5
[17] RCurl_1.95-4.1     Rsamtools_1.13.17  rtracklayer_1.21.5 
scales_0.2.3
[21] stats4_3.0.1       stringr_0.6.2      tools_3.0.1 
XML_3.95-0.2
[25] zlibbioc_1.7.0