[BioC] autoplot() in ggbio package for txdb object

[Tengfei Yin]

Hi Rebecca,

So sorry for the late reply, in case I forget next time, please feel free
to leave your question/feedback in github issues page backlog
<https://github.com/tengfei/ggbio/issues>. I will work on those issues when
I got time.

For you question, yes, I just confirmed this is a bug in biovizBase/ggbio
package for exons with no cds, I fixed the released branch
biovizBase(1.12.2) and ggbio(1.12.9) (will fix the devel branch later this
week), please update your packages two days later to see if my fix solved
the problem or not.

thanks again for reporting the bug!

cheers


On Tue, Jul 8, 2014 at 1:55 PM, sun <fireflysrb at gmail.com> wrote:

> Hello,
>
> I tried to draw the gene model by using autoplot() in ggbio package with
> the following codes.
>
> library(ggbio)
> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> data(genesymbol, package =   "biovizBase")
> autoplot(txdb,which = genesymbol["ACSS2"],names.expr ="tx_name")
>
> There is only one straight line and no any exons displayed for
> "uc010zum.1", which actually has 6 exons. Anything wrong?
>
> exons <- exonsBy(txdb, "tx",use.names=TRUE)
> exons[which(names(exons)=="uc010zum.1")]
> GRangesList of length 1:
> $uc010zum.1
> GRanges with 6 ranges and 3 metadata columns:
>       seqnames               ranges strand |   exon_id   exon_name
> exon_rank
>          <Rle>            <IRanges>  <Rle> | <integer> <character>
> <integer>
>   [1]    chr20 [33464328, 33464626]      + |    252380        <NA>
>  1
>   [2]    chr20 [33470597, 33470792]      + |    252381        <NA>
>  2
>   [3]    chr20 [33511126, 33511234]      + |    252394        <NA>
>  3
>   [4]    chr20 [33513501, 33513569]      + |    252395        <NA>
>  4
>   [5]    chr20 [33513908, 33514084]      + |    252396        <NA>
>  5
>   [6]    chr20 [33514680, 33514754]      + |    252397        <NA>
>  6
>
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (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] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] XVector_0.4.0
> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
> GenomicFeatures_1.16.2
>  [4] AnnotationDbi_1.26.0
> Biobase_2.24.0
> GenomicRanges_1.16.3
>  [7] GenomeInfoDb_1.0.2
> IRanges_1.22.9
> ggbio_1.12.8
> [10] ggplot2_1.0.0
> BiocGenerics_0.10.0
>
> Thanks,
>
> Rebecca
>
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>
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-- 
Tengfei Yin, PhD
Product Manager
Seven Bridges Genomics
sbgenomics.com
One Broadway FL 7
Cambridge, MA 02142
(617) 866-0446

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