hi,

I would like to use Gviz with the mitochondrial chromosome chrM but I get the following error when calling IdeogramTrack():

library(Gviz)

itrack <- IdeogramTrack(genome="hg19", chromosome="chrM")
Error in .normargSeqlevels(seqnames) :
  supplied 'seqlevels' cannot contain NAs or empty strings ("")

traceback()
10: stop(errmsg)
9: .normargSeqlevels(seqnames)
8: Seqinfo(names(seqlengths), seqlengths)
7: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand,
       mcols = DataFrame(...), seqlengths = seqlengths, seqinfo = seqinfo)
6: GRanges(seqnames = bnames, range = IRanges(start = bands$chromStart,
       end = bands$chromEnd), name = bnames, type = as.character(bands$gieStain))
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("IdeogramTrack", chromosome = chromosome, genome = genome,
       name = name, bands = bands, ...)
1: IdeogramTrack(genome = "hg19", chromosome = "chrM")

The error seems a bit cryptic so I guess that rather than a limiting feature this may be something related to a malformation of the underlying GRanges object.

thanks in advance!

robert.

sessionInfo()
R version 3.1.1 Patched (2014-10-13 r66751)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8    
 [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8   
 [7] LC_PAPER=en_US.UTF8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C      

attached base packages:
 [1] stats4    parallel  grid      stats     graphics
 [6] grDevices utils     datasets  methods   base     

other attached packages:
 [1] Gviz_1.10.9          GenomicRanges_1.18.4
 [3] GenomeInfoDb_1.2.4   IRanges_2.0.1       
 [5] S4Vectors_0.4.0      BiocGenerics_0.12.1
 [7] BiocInstaller_1.16.1 vimcom_1.0-0        
 [9] setwidth_1.0-3       colorout_1.0-3      

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.28.1    
 [3] base64enc_0.1-2          BatchJobs_1.5           
 [5] BBmisc_1.9               Biobase_2.26.0          
 [7] BiocParallel_1.0.3       biomaRt_2.22.0          
 [9] Biostrings_2.34.1        biovizBase_1.14.1       
[11] bitops_1.0-6             brew_1.0-6              
[13] BSgenome_1.34.1          checkmate_1.5.1         
[15] cluster_2.0.1            codetools_0.2-10        
[17] colorspace_1.2-4         DBI_0.3.1               
[19] dichromat_2.0-0          digest_0.6.8            
[21] fail_1.2                 foreach_1.4.2           
[23] foreign_0.8-63           Formula_1.2-0           
[25] GenomicAlignments_1.2.1  GenomicFeatures_1.18.3  
[27] ggplot2_1.0.0            gtable_0.1.2            
[29] Hmisc_3.15-0             iterators_1.0.7         
[31] lattice_0.20-30          latticeExtra_0.6-26     
[33] MASS_7.3-39              matrixStats_0.14.0      
[35] munsell_0.4.2            nnet_7.3-9              
[37] plyr_1.8.1               proto_0.3-10            
[39] RColorBrewer_1.1-2       Rcpp_0.11.4             
[41] RCurl_1.95-4.5           reshape2_1.4.1          
[43] rpart_4.1-9              Rsamtools_1.18.2        
[45] RSQLite_1.0.0            rtracklayer_1.26.2      
[47] scales_0.2.4             sendmailR_1.2-1         
[49] splines_3.1.1            stringr_0.6.2           
[51] survival_2.37-7          tools_3.1.1             
[53] VariantAnnotation_1.12.9 XML_3.98-1.1            
[55] XVector_0.6.0            zlibbioc_1.12.0         

Should be fixed in  version 1.10.10

Hi Robert,

yes, the 'name' column of the bands information for the mitochondrial chromosome is an empty string, and GRanges chokes on that:

Browse[3]> bands
    chrom chromStart chromEnd name gieStain
455  chrM          0    16571          gneg

I will commit a fix to this soon. Thanks for reporting.

Florian