[BioC] ggbio error: Objects of type OrganismDb not supported by autoplot

[Tengfei Yin]

Hey Jim,

Thanks for your reply! Warning is fine, I removed the warning in the new
version, it's just internally there is a "gap" in the type column as a
byproduct; but in practice, you can you specify exons, cds, utr, the
introns will be inferred, so no need for 'gap' type.

Hey Georg

So sorry for the late response Georg, I think like Jim point out, the
latest version will fix the problem.

cheers

Tengfei


On Fri, Aug 22, 2014 at 10:05 AM, James W. MacDonald <jmacdon at uw.edu> wrote:

> Hi Georg,
>
> Update to the current version of R and ggbio:
>
> > autoplot(Homo.sapiens, which = wh)
> Error: Objects of type OrganismDb not supported by autoplot.  Please use
> qplot() or ggplot() instead.
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> <snip>
>
> But with the current versions:
>
> > autoplot(Homo.sapiens, which = wh)
> Parsing transcripts...
> Parsing exons...
> Parsing cds...
> Parsing utrs...
> ------exons...
> ------cdss...
> ------introns...
> ------utr...
> aggregating...
> Done
> "gap" is not matching to following arbitrary model terms"cds CDS Cds exon
> EXON Exon utr UTR Utr"
> Constructing graphics...
> Warning message:
> Removed 2 rows containing missing values (geom_text).
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> Best,
>
> Jim
>
>
>
>
>
> On Thu, Aug 21, 2014 at 11:05 AM, Georg Otto <georg.otto at imm.ox.ac.uk>
> wrote:
>
> > Dear all,
> >
> > I have a problem reproducing the vignette of the ggbio package:
> >
> > > library(ggbio)
> > > library(Homo.sapiens)
> > > class(Homo.sapiens)
> > [1] "OrganismDb"
> > attr(,"package")
> > [1] "OrganismDbi"
> > > data(genesymbol, package = "biovizBase")
> > > wh <- genesymbol[c("BRCA1", "NBR1")]
> > > wh <- range (wh, ignore.strand = TRUE)
> > > p.txdb <- autoplot(Homo.sapiens, which = wh)
> > Error: Objects of type OrganismDb not supported by autoplot.  Please use
> > qplot() or ggplot() instead.
> >
> > Can anybody tell me what is going on?
> >
> > Best wishes,
> >
> > Georg
> >
> > > sessionInfo()
> > R version 3.0.1 (2013-05-16)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> >  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> >  [7] LC_PAPER=C                 LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> >  [1] Homo.sapiens_1.1.2
> >  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
> >  [3] org.Hs.eg.db_2.10.1
> >  [4] GO.db_2.10.1
> >  [5] RSQLite_0.11.4
> >  [6] DBI_0.2-7
> >  [7] OrganismDbi_1.4.0
> >  [8] GenomicFeatures_1.14.5
> >  [9] AnnotationDbi_1.24.0
> > [10] Biobase_2.22.0
> > [11] ggbio_1.10.16
> > [12] ggplot2_1.0.0
> > [13] plyr_1.8.1
> > [14] Rsamtools_1.14.3
> > [15] Biostrings_2.30.1
> > [16] GenomicRanges_1.14.4
> > [17] XVector_0.2.0
> > [18] IRanges_1.20.7
> > [19] BiocGenerics_0.8.0
> >
> > loaded via a namespace (and not attached):
> >  [1] biomaRt_2.18.0           biovizBase_1.10.8        bitops_1.0-6
> >  [4] BSgenome_1.30.0          cluster_1.15.2           colorspace_1.2-4
> >  [7] compiler_3.0.1           dichromat_2.0-0          digest_0.6.4
> > [10] Formula_1.1-2            graph_1.40.1             grid_3.0.1
> > [13] gridExtra_0.9.1          gtable_0.1.2             Hmisc_3.14-4
> > [16] lattice_0.20-29          latticeExtra_0.6-26      MASS_7.3-33
> > [19] munsell_0.4.2            proto_0.3-10             RBGL_1.38.0
> > [22] RColorBrewer_1.0-5       Rcpp_0.11.2              RCurl_1.95-4.3
> > [25] reshape2_1.4             rtracklayer_1.22.7       scales_0.2.4
> > [28] splines_3.0.1            stats4_3.0.1             stringr_0.6.2
> > [31] survival_2.37-7          tools_3.0.1
> > VariantAnnotation_1.8.13
> > [34] XML_3.98-1.1             zlibbioc_1.8.0
> >
> >
> > --
> > Georg Otto
> > The Weatherall Institute of Molecular Medicine
> > Oxford, UK
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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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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