[BioC] Error with autoplot of transcriptDB object

[Mark Dunning]

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

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