[BioC] autoplot transcriptDb error with some regions

Alejandro Reyes alejandro.reyes at embl.de
Tue Oct 22 10:12:16 CEST 2013


Hi Tengfei,

Thanks for the fix! It does not give an error anymore, however, in the 
case below, the lines representing the introns (e.g. ---->---->---->---) 
are not being plotted. I am getting a warning as well, see case below:

 > suppressMessages( library(ggbio) )
 > suppressMessages(library(GenomicFeatures))
 > tx <- makeTranscriptDbFromBiomart()
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
 >

This works great:

 >
 > 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...
 >

This does not draw the introns and produces a warning:

 >
 > 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...
Done
Constructing graphics...
Warning message:
In ans[] <- x :
   number of items to replace is not a multiple of replacement length

 > sessionInfo()

R Under development (unstable) (2013-10-21 r64088)
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] GenomicFeatures_1.15.0 AnnotationDbi_1.25.0 Biobase_2.23.1
  [4] GenomicRanges_1.15.1   XVector_0.3.0 IRanges_1.21.2
  [7] BiocGenerics_0.9.0     ggbio_1.11.1 ggplot2_0.9.3.1
[10] BiocInstaller_1.13.1

loaded via a namespace (and not attached):
  [1] biomaRt_2.19.0          Biostrings_2.31.0 biovizBase_1.11.1
  [4] bitops_1.0-6            BSgenome_1.31.0 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_1.15.2        RSQLite_0.11.4 rtracklayer_1.23.1
[28] scales_0.2.3            stats4_3.1.0 stringr_0.6.2
[31] tools_3.1.0             VariantAnnotation_1.9.3 XML_3.98-1.1
[34] zlibbioc_1.9.0


Thanks again and let me know if you need additional information!

Alejandro



> Hi Alejandro,
>
> I fixed the bug in devel branch, may be updated one day later, please 
> try again to see if that fix works for you.
>
> I recently changed Txdb plot, and other features, actually don't have 
> time to update vignettes accordingly yet, please let me know if you 
> have further problem, I will try my best to fix it asap.
>
> Thanks
>
> Tengfei
>
>
> On Fri, Oct 18, 2013 at 1:05 PM, Tengfei Yin 
> <tengfei.yin at sbgenomics.com <mailto:tengfei.yin at sbgenomics.com>> wrote:
>
>     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 at embl.de <mailto:alejandro.reyes at 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 <http://sbgenomics.com/>
>     625 Mt. Auburn St. Suite #208
>     Cambridge, MA 02138
>     (617) 866-0446
>
>
>
>
> -- 
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com <http://sbgenomics.com/>
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866-0446



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