Hi all, I've having problems running some code that was previously Ok for me. Can anyone see what is going wrong? Did ggbio change how it plots transcripts? Regards, Mark >library(TxDb.Hsapiens.UCSC.hg19.knownGene) >txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >exons <- exonsBy(txdb, "gene") >ibrary(ggbio) >autoplot(txdb,which=exons[["49"]]) Parsing transcripts... Parsing exons... Parsing cds... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done "gap" is not matching to following arbitrary model terms"cds CDS Cds exon EXON Exon utr UTR Utr" Constructing graphics... Error in `[[<-`(`*tmp*`, name, value = 1L) : 1 elements in value to replace 0 elements > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.4.0 ggbio_1.12.10 [3] ggplot2_1.0.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 [5] GenomicFeatures_1.16.2 AnnotationDbi_1.26.0 [7] Biobase_2.24.0 GenomicRanges_1.16.4 [9] GenomeInfoDb_1.0.2 IRanges_1.22.10 [11] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.3 BBmisc_1.7 BiocParallel_0.6.1 biomaRt_2.20.0 [5] Biostrings_2.32.1 biovizBase_1.12.3 bitops_1.0-6 brew_1.0-6 [9] BSgenome_1.32.0 checkmate_1.3 cluster_1.15.2 codetools_0.2-9 [13] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [17] fail_1.2 foreach_1.4.2 Formula_1.1-2 GenomicAlignments_1.0.6 [21] grid_3.1.1 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 [25] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-34 [29] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 RColorBrewer_1.0-5 [33] Rcpp_0.11.2 RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.1 [37] RSQLite_0.11.4 rtracklayer_1.24.2 scales_0.2.4 sendmailR_1.1-2 [41] splines_3.1.1 stats4_3.1.1 stringr_0.6.2 survival_2.37-7 [45] tools_3.1.1 VariantAnnotation_1.10.5 XML_3.98-1.1 zlibbioc_1.10.0 [[alternative HTML version deleted]]

----- Original Message ----- > From: "Mark Dunning" <mark.dunning@gmail.com> > To: bioconductor@r-project.org > Sent: Wednesday, September 3, 2014 3:16:06 AM > Subject: [BioC] Error with autoplot of transcriptDB object > > Hi all, > > I've having problems running some code that was previously Ok for me. > Can > anyone see what is going wrong? Did ggbio change how it plots > transcripts? > > Regards, > > Mark > > >library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >exons <- exonsBy(txdb, "gene") > >ibrary(ggbio) > > >autoplot(txdb,which=exons[["49"]]) > > Parsing transcripts... > Parsing exons... > Parsing cds... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > "gap" is not matching to following arbitrary model terms"cds CDS Cds > exon > EXON Exon utr UTR Utr" > Constructing graphics... > Error in `[[<-`(`*tmp*`, name, value = 1L) : > 1 elements in value to replace 0 elements > > > I don't have a solution but I'll add that the same code works fine for me in devel but fails consistently in release. When it fails in release, traceback() indicates that the problem is happening somewhere in the geom_alignment method in ggbio (cc'ing Tengfei). Here's my sessionInfo() from running this same code in devel where it works fine: R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] XVector_0.5.8 [2] ggbio_1.13.13 [3] ggplot2_1.0.0 [4] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 [5] GenomicFeatures_1.17.14 [6] AnnotationDbi_1.27.10 [7] Biobase_2.25.0 [8] GenomicRanges_1.17.40 [9] GenomeInfoDb_1.1.19 [10] IRanges_1.99.28 [11] S4Vectors_0.2.4 [12] BiocGenerics_0.11.5 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 BatchJobs_1.3 [3] BBmisc_1.7 BiocParallel_0.99.19 [5] biomaRt_2.21.1 Biostrings_2.33.14 [7] biovizBase_1.13.10 bitops_1.0-6 [9] brew_1.0-6 BSgenome_1.33.9 [11] checkmate_1.4 cluster_1.15.3 [13] codetools_0.2-9 colorspace_1.2-4 [15] DBI_0.3.0 dichromat_2.0-0 [17] digest_0.6.4 fail_1.2 [19] foreach_1.4.2 foreign_0.8-61 [21] Formula_1.1-2 GenomicAlignments_1.1.29 [23] GGally_0.4.8 graph_1.43.0 [25] grid_3.1.1 gridExtra_0.9.1 [27] gtable_0.1.2 Hmisc_3.14-5 [29] iterators_1.0.7 labeling_0.3 [31] lattice_0.20-29 latticeExtra_0.6-26 [33] MASS_7.3-34 munsell_0.4.2 [35] nnet_7.3-8 OrganismDbi_1.7.5 [37] plyr_1.8.1 proto_0.3-10 [39] RBGL_1.41.1 RColorBrewer_1.0-5 [41] Rcpp_0.11.2 RCurl_1.95-4.3 [43] reshape_0.8.5 reshape2_1.4 [45] rpart_4.1-8 Rsamtools_1.17.33 [47] RSQLite_0.11.4 rtracklayer_1.25.16 [49] scales_0.2.4 sendmailR_1.1-2 [51] splines_3.1.1 stringr_0.6.2 [53] survival_2.37-7 tools_3.1.1 [55] VariantAnnotation_1.11.34 XML_3.98-1.1 [57] zlibbioc_1.11.1 Dan > > > sessionInfo() > R version 3.1.1 (2014-07-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods > base > > other attached packages: > [1] XVector_0.4.0 > ggbio_1.12.10 > [3] ggplot2_1.0.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > [5] GenomicFeatures_1.16.2 > AnnotationDbi_1.26.0 > [7] Biobase_2.24.0 > GenomicRanges_1.16.4 > [9] GenomeInfoDb_1.0.2 > IRanges_1.22.10 > [11] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.3 BBmisc_1.7 > BiocParallel_0.6.1 biomaRt_2.20.0 > [5] Biostrings_2.32.1 biovizBase_1.12.3 > bitops_1.0-6 brew_1.0-6 > [9] BSgenome_1.32.0 checkmate_1.3 > cluster_1.15.2 codetools_0.2-9 > [13] colorspace_1.2-4 DBI_0.2-7 > dichromat_2.0-0 digest_0.6.4 > [17] fail_1.2 foreach_1.4.2 > Formula_1.1-2 GenomicAlignments_1.0.6 > [21] grid_3.1.1 gridExtra_0.9.1 > gtable_0.1.2 Hmisc_3.14-4 > [25] iterators_1.0.7 lattice_0.20-29 > latticeExtra_0.6-26 MASS_7.3-34 > [29] munsell_0.4.2 plyr_1.8.1 > proto_0.3-10 RColorBrewer_1.0-5 > [33] Rcpp_0.11.2 RCurl_1.95-4.1 > reshape2_1.4 Rsamtools_1.16.1 > [37] RSQLite_0.11.4 rtracklayer_1.24.2 > scales_0.2.4 sendmailR_1.1-2 > [41] splines_3.1.1 stats4_3.1.1 > stringr_0.6.2 survival_2.37-7 > [45] tools_3.1.1 VariantAnnotation_1.10.5 > XML_3.98-1.1 zlibbioc_1.10.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor