Hi Alejandro,

Thanks for reporting, I believe that's a bug caused by my recent
modification in biovizBase package, I am working on that now, will keep you
updated.

Best

Tengfei


On Fri, Oct 18, 2013 at 12:43 PM, Alejandro Reyes
<alejandro.reyes@embl.de>wrote:

> 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
>



-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

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