[BioC] Gviz: Error plotting C.elegans ideogram

[Michael Dondrup]

Just found the obvious.

The error is caused by the fact that the c.elegans genome doesn't have a cytoband track. Not all genomes have this 
track. Maybe the error message could be made more clear, something like:
"There is no cytoband information for chromosome 1 in UCSC genome 'ce4'"

Cheers
Michael

On Jun 22, 2012, at 2:20 PM, Michael Dondrup wrote:

> Hi,
> 
> I am trying to plot an ideogram track for C. elegans using Gviz. However I cannot generate the ideogram track:
> 
>> itrack <- IdeogramTrack(genome = "ce6", chromosome = "chrI" )
> Error in normArgTrack(track, trackids) : Unknown track: cytoBandIdeo
> 
> I have tried also "ce4, and ce10" and for the chromosome "chr1, chrII, 1" with the same effect.
> Other genomes (hgu19, mm9) worked. Do I have to use a different genome identifier?
> 
> Best
> Michael Dondrup
> 
>> 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] grid      stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] IRanges_1.14.3     BiocGenerics_0.2.0 Gviz_1.0.1        
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.18.1 Biobase_2.16.0       biomaRt_2.12.0       Biostrings_2.24.1    bitops_1.0-4.1       BSgenome_1.24.0     
> [7] DBI_0.2-5            GenomicRanges_1.8.6  lattice_0.20-6       RColorBrewer_1.0-5   RCurl_1.91-1         Rsamtools_1.8.5     
> [13] RSQLite_0.11.1       rtracklayer_1.16.1   stats4_2.15.0        tools_2.15.0         XML_3.9-4            zlibbioc_1.2.0      
>> 
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