I am using package Gviz to plot genomic regions for rat data. I have got an error:

> biomTrack_test<-BiomartGeneRegionTrack(genome="Rnor_6.0",chromosome=12, start=20000000,end=25000000,name="ENSEMBL",showId=T)
Error in .genome2Dataset(genome) : 
  Unable to automatically determine Biomart data set for UCSC genome identifier 'Rnor_6.0'.
Please manually provide biomaRt object

When I chose the human genome there is no problem:

> biomTrack_test<-BiomartGeneRegionTrack(genome="hg19",chromosome=12, start=20000000,end=25000000,name="ENSEMBL",showId=T)
> trackList<-c(trackList,biomTrack_test)

> listMarts()

1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 84
2     ENSEMBL_MART_SNP  Ensembl Variation 84
> ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl")
> listDatasets(ensembl)[1:10,]
                          dataset                                description
8             fcatus_gene_ensembl        Felis catus genes (Felis_catus_6.2)
9        rnorvegicus_gene_ensembl         Rattus norvegicus genes (Rnor_6.0)

What is my problem?

Thank you for any suggestions,

Best regards,

Monika

May I suggest an alternative that doesn't require biomart? You could create an EnsDb database with all the annotations for rat from Ensembl and use that to fetch data to plot. The easiest way is outlined below, i.e. using AnnotationHub to fetch the GTF file from Ensembl that contains the annotation. You can create an EnsDb object (eventually also a package using the makeEnsembldbPackage function, so you don't have to create the db each time) and use that to retrieve data for Gviz:

library(AnnotationHub)
library(Gviz)
library(ensembldb)

## List all rat GTF files from Ensembl:
ah <- AnnotationHub()
query(ah, c("ensembl", "gtf", "rnor"))

AnnotationHub with 14 records
# snapshotDate(): 2016-06-06
# $dataprovider: Ensembl
# $species: Rattus norvegicus
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
#   sourcetype
# retrieve records with, e.g., 'object[["AH7583"]]'

            title                            
  AH7583  | Rattus_norvegicus.Rnor_5.0.70.gtf
  AH7691  | Rattus_norvegicus.Rnor_5.0.71.gtf
  AH7752  | Rattus_norvegicus.Rnor_5.0.72.gtf
  ...       ...                              
  AH47992 | Rattus_norvegicus.Rnor_6.0.81.gtf
  AH50337 | Rattus_norvegicus.Rnor_6.0.82.gtf
  AH50406 | Rattus_norvegicus.Rnor_6.0.83.gtf

## Let's select the one for Ensembl 83 and create the annotation database:
dbFile <- ensDbFromAH(ah["AH50406"])
edb <- EnsDb(dbFile)

## Create the GeneTrack
gTrack <- getGeneRegionTrackForGviz(edb, filter=GRangesFilter(seqnames=12, IRanges(start=20000000, end=25000000)))

## Plot the data
plotTracks(list(GenomeAxisTrack(), GeneRegionTrack(gTrack)), transcriptAnnotation="symbol")

hope that helps too.

cheers, jo

Here is the hint that Gviz is giving you:

Unable to automatically determine Biomart data set for UCSC genome identifier 'Rnor_6.0'.
Please manually provide biomaRt object

And if you look at ?BiomartGeneRegionTrack (which you should!) you will see

 biomart: An optional 'Mart' object providing access to the EBI Biomart
          webservice. As default the appropriate Ensembl data source is
          selected based on the provided genome and chromosome.

Which is, like, another hint, and indicates that probably you need to provide that information.

> library(Gviz)
> library(biomaRt)
> mart <- useMart("ENSEMBL_MART_ENSEMBL","rnorvegicus_gene_ensembl")
> biomTrack_test<-BiomartGeneRegionTrack(genome="Rnor_6.0",chromosome=12, start=20000000,end=25000000,name="ENSEMBL",showId=T, biomart = mart)
Warning message:
In .local(x, ..., na.rm = na.rm) : 'na.rm' argument is ignored
> biomTrack_test
GeneRegionTrack 'ENSEMBL'
| genome: Rnor_6.0
| active chromosome: chr12
| annotation features: 3163

And just to check and stuff

> z <- listDatasets(mart)
> z[grep("rnorvegicus", z[,1]),]
                   dataset                        description  version
9 rnorvegicus_gene_ensembl Rattus norvegicus genes (Rnor_6.0) Rnor_6.0
>