[BioC] autoplot transcriptDb error with some regions

[Alejandro Reyes]

Dear Tengfei Yin,

Firstly, thanks for developing ggbio, it has been very useful for me!

I am getting an error when using autoplot with some specific genomic 
regions in transcriptDb objects, here is an example:

 > suppressMessages( library(ggbio) )
 > suppressMessages(library(GenomicFeatures))
 > tx <- makeTranscriptDbFromBiomart()

Aggregating TranscriptDb...
Parsing exons...
Parsing cds...
Parsing transcripts...
Parsing utrs and aggregating...
Done
Constructing graphics...

prueba <- GRanges( 16, IRanges( start=69598997, 69718569 ) )
autoplot( tx, prueba, group.selfish=TRUE, names.expr="")

Aggregating TranscriptDb...
Parsing exons...
Parsing cds...
Parsing transcripts...
Parsing utrs and aggregating...
Done
Constructing graphics...

So far, excellent, however, when I look into a smaller region I get an 
error message:

 > prueba <- GRanges( "16", IRanges(start=69718724, end=69720078 ))
 > autoplot( tx, prueba, group.selfish=TRUE, names.expr="")
Aggregating TranscriptDb...
Parsing exons...
Parsing cds...
Parsing transcripts...
Parsing utrs and aggregating...
Error in DataFrame(...) : different row counts implied by arguments

I believe it has to do with recent modifications of ggbio, since I do 
not get the error message with older versions, e.g. 1.9.7.

 > sessionInfo()
R Under development (unstable) (2013-07-01 r63121)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
  [1] ggbio_1.11.0           ggplot2_0.9.3.1 GenomicFeatures_1.15.0
  [4] AnnotationDbi_1.23.28  Biobase_2.21.7 GenomicRanges_1.13.56
  [7] XVector_0.1.4          IRanges_1.19.40 BiocGenerics_0.7.8
[10] BiocInstaller_1.13.1

loaded via a namespace (and not attached):
  [1] biomaRt_2.17.3           Biostrings_2.29.19 biovizBase_1.9.4
  [4] bitops_1.0-6             BSgenome_1.29.1 cluster_1.14.4
  [7] colorspace_1.2-4         DBI_0.2-7 dichromat_2.0-0
[10] digest_0.6.3             grid_3.1.0 gridExtra_0.9.1
[13] gtable_0.1.2             Hmisc_3.12-2 labeling_0.2
[16] lattice_0.20-24          MASS_7.3-29 munsell_0.4.2
[19] plyr_1.8                 proto_0.3-10 RColorBrewer_1.0-5
[22] RCurl_1.95-4.1           reshape2_1.2.2 rpart_4.1-3
[25] Rsamtools_1.13.53        RSQLite_0.11.4 rtracklayer_1.21.14
[28] scales_0.2.3             stats4_3.1.0 stringr_0.6.2
[31] tools_3.1.0              VariantAnnotation_1.7.57 XML_3.98-1.1
[34] zlibbioc_1.7.0

Best regards,
Alejandro Reyes