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Question: Gviz error with collapseTranscripts=TRUE
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gravatar for Stephanie M. Gogarten
5.2 years ago by
University of Washington
Stephanie M. Gogarten560 wrote:
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
ADD COMMENTlink modified 5.1 years ago by florian.hahne@novartis.com1.6k • written 5.2 years ago by Stephanie M. Gogarten560
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gravatar for florian.hahne@novartis.com
5.1 years ago by
Switzerland
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))
ADD COMMENTlink written 5.1 years ago by florian.hahne@novartis.com1.6k
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gravatar for florian.hahne@novartis.com
5.1 years ago by
Switzerland
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))
ADD COMMENTlink written 5.1 years ago by florian.hahne@novartis.com1.6k
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