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

Hi Stephanie, thanks for reporting this. I can reproduce the issue and will look at a fix soon. Will let you know, Florian On 6/10/13 8:56 PM, "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu=""> wrote: >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))

Stephanie, this should be fixed now in version 1.5.6 in the development branch and version 1.4.3 in the release branch. Thanks again for reporting this. Florian On 6/10/13 8:56 PM, "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu=""> wrote: >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))