Question: Gviz: Error plotting C.elegans ideogram
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gravatar for Michael Dondrup
7.4 years ago by
Michael Dondrup550 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 >
ideogram genomes gviz • 835 views
ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Michael Dondrup550
Answer: Gviz: Error plotting C.elegans ideogram
0
gravatar for Michael Dondrup
7.4 years ago by
Michael Dondrup550 wrote:
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 >> > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.4 years ago by Michael Dondrup550
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