Hi Michael,

The qplot generic has been replaced with "autoplot".

On Fri, Jul 6, 2012 at 10:44 AM, Michael Muratet
<mmuratet@hudsonalpha.org>wrote:

> Greetings
>
> I installed a development version of bioconductor to get the
> distanceToNearest functionality (sessionInfo below). I am trying to plot a
> GRanges object with ggbio
>
> > is(hits)
> [1] "GRanges"                    "GenomicRanges"              "Vector"
>                 "GenomicRangesORmissing"     "GenomicRangesORGRangesList"
> [6] "RangedDataORGenomicRanges"  "Annotated"
>
> > p <- qplot(hits)
> > print(p)
> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>   cannot coerce class 'structure("GRanges", package = "GenomicRanges")'
> into a data.frame
>
> I haven't been able to track down the problem. Have I created a
> compatibility issue with the development version? Is it operator error? I
> could save the object and go back to release versions.
>
> Thanks for the help
>
> Mike
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] ggbio_1.5.6            ggplot2_0.9.1          BiocInstaller_1.5.11
> rtracklayer_1.17.11    GenomicFeatures_1.9.19 AnnotationDbi_1.19.16
>  [7] Biobase_2.17.6         GenomicRanges_1.9.29   IRanges_1.15.17
>  BiocGenerics_0.3.0
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.13.1           Biostrings_2.25.6        biovizBase_1.5.2
>       bitops_1.0-4.1           BSgenome_1.25.3          cluster_1.14.2
>  [7] colorspace_1.1-1         DBI_0.2-5                dichromat_1.2-4
>      digest_0.5.2             grid_2.15.0              gridExtra_0.9
> [13] Hmisc_3.9-3              labeling_0.1             lattice_0.20-6
>       MASS_7.3-19              Matrix_1.0-6             memoise_0.1
> [19] munsell_0.3              plyr_1.7.1               proto_0.3-9.2
>      RColorBrewer_1.0-5       RCurl_1.91-1             reshape2_1.2.1
> [25] Rsamtools_1.9.19         RSQLite_0.11.1           scales_0.2.1
>       snpStats_1.7.2           splines_2.15.0           stats4_2.15.0
> [31] stringr_0.6              survival_2.36-14         tools_2.15.0
>       VariantAnnotation_1.3.16 XML_3.9-4                zlibbioc_1.3.0
>
>
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet@hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
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