[BioC] Error with autoplot of transcriptDB object
Dan Tenenbaum
dtenenba at fhcrc.org
Mon Sep 15 19:02:15 CEST 2014
----- Original Message -----
> From: "Mark Dunning" <mark.dunning at gmail.com>
> To: bioconductor at 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
>
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>
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