ggbio error: Objects of type OrganismDb not supported by autoplot

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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