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

[James W. MacDonald]

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
>
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-- 
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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