Hi all,

I have a downloaded a BioMartGeneRegionTrack. I want know to plot two gene names simultaneously, e.g.. "NM_12345" and ""uc1234.abc.1". I have used biomaRt to get the according information for the gene to plot:

gene_names <- getBM(attributes = c("refseq_mrna","ucsc"),filters="refseq_mrna",values=refseqids,mart=ensembl)

Does anyone know how to proceed at this point?

Best, Angela

You will not be able to do this using a BiomartGeneRegionTrack. That is really just a wrapper around Biomart calls serving as an abstraction layer to the more advanced features of a native GeneRegionTrack. I'd suggest that you use that class instead. There are plenty of ways how you could instantiate the object from your BiomartGeneRegionTrack object, the easiest is:

bmTrack <- as(bmTrack, "GeneRegionTrack")

Gviz does not allow to use say both the transcript identifier and the gene symbol as feature annotation, but of course you are free to assign any values you like to either the transcript, gene or symbol properties. For instance, this will add the string 'transcript ' in front of the existing transcript identifiers:

transcript(bmTrack) <- paste("transcript", transcript(bmTrack))

Hope that gets you started,

Florian