Hi all,

I'm trying to plot an ideogram for the "dm3" genome using ggbio. I believe
the following should work (it did for previous version of BioC).

plotIdeogram(genome = "dm3")

However, I get an error.

Error in FUN("dm3"[[1L]], ...) : object 'cytobands' not found


In the code I can't see where cytobands is defined. How can I get the
ideogram for dm3.

Regards,

Mark

Ideogram(obj, xlabel = xlabel, subchr = subchr, aspect.ratio = aspect.ratio,
    color = color, fill = fill, alpha = alpha, size = size,
zoom.region = zoom.region,
    zoom.offset = zoom.offset, genome = genome)
debug: {
    if (missing(obj)) {
        data(ideoCyto, package = "biovizBase")
        if (genome %in% names(ideoCyto)) {
            obj <- ideoCyto[[genome]]
        }
        else {
            obj <- getIdeogram(genome = genome, subchr = subchr,
                cytobands = cytobands)




> sessionInfo()R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
LC_TIME=en_GB.UTF-8
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8
LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
[1] rtracklayer_1.24.2   GenomicRanges_1.16.2 GenomeInfoDb_1.0.2
IRanges_1.22.4
[5] ggbio_1.12.8         ggplot2_1.0.0        BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0     BatchJobs_1.2            BBmisc_1.6
 [4] Biobase_2.24.0           BiocParallel_0.6.0       biomaRt_2.20.0
 [7] Biostrings_2.32.1        biovizBase_1.12.1        bitops_1.0-6
[10] brew_1.0-6               BSgenome_1.32.0          cluster_1.15.2
[13] codetools_0.2-8          colorspace_1.2-4         DBI_0.2-7
[16] dichromat_2.0-0          digest_0.6.4             fail_1.2
[19] foreach_1.4.1            Formula_1.1-1            GenomicAlignments_1.0.0
[22] GenomicFeatures_1.16.0   grid_3.1.0               gridExtra_0.9.1
[25] gtable_0.1.2             Hmisc_3.14-4             iterators_1.0.6
[28] lattice_0.20-29          latticeExtra_0.6-26      MASS_7.3-32
[31] munsell_0.4.2            plyr_1.8.1               proto_0.3-10
[34] RColorBrewer_1.0-5       Rcpp_0.11.1              RCurl_1.95-4.1
[37] reshape2_1.4             Rsamtools_1.16.0         RSQLite_0.11.4
[40] scales_0.2.4             sendmailR_1.1-2          splines_3.1.0
[43] stats4_3.1.0             stringr_0.6.2            survival_2.37-7
[46] tools_3.1.0              VariantAnnotation_1.10.0 XML_3.98-1.1
[49] XVector_0.4.0            zlibbioc_1.10.0

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