Hi Alejandro,

Would you mind send me a picture of that (off mailing list is ok), do you
just see a utr and exons? I want to make sure how it looks like, there are
two possible reason for that
1. you pass xlim in autoplot, it will cut the data
2. I think you just want to zoom into the region to check details, and keep
introns and everyting, you probably need to generate a larger region and
use +xlim(granges) to zoom in without cutting any data.

I am not sure is that due to the above reason or new bugs, so the picture
will help.

Thanks

Tengfei


On Tue, Oct 22, 2013 at 4:12 AM, Alejandro Reyes <alejandro.reyes@embl.de>wrote:

> 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@sbgenomics.com<mailto:
>> tengfei.yin@**sbgenomics.com <tengfei.yin@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@embl.de <mailto:alejandro.reyes@embl.**de<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 <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
>>
>
>


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

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