Hi everybody,
I am currently trying to add a BiomartGeneRegionTrack to my figure showing the gene model and the gene symbol. Using the following lines of code I am already getting a nice graphic representation of the gene model, however the gene symbols are present in symbol(bmt) but aren't plotted in the figure by adding transcriptAnnotation = "symbol" to plotTracks(). Possibly I misunderstood something in the usage of transcriptAnnotation?
gen <- "mm10"
afrom <- 45298258
ato <- 45340790
chr <- "7"
bmt <- BiomartGeneRegionTrack(genome=gen, chromosome=chr, start=afrom, end=ato, stacking="dense")
symbol(bmt)
plotTracks(bmt, from=afrom, to=ato, chromosome=chr, transcriptAnnotation = "symbol")
Here is my SessionInfo. I would be very grateful for some advice!
Best,
Broder
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] XVector_0.6.0 Gviz_1.10.10 GenomicRanges_1.18.4 GenomeInfoDb_1.2.2
[5] IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.0
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2
[4] BatchJobs_1.5 BBmisc_1.9 Biobase_2.26.0
[7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.0
[10] biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.0 checkmate_1.5.1 cluster_2.0.1
[16] codetools_0.2-11 colorspace_1.2-6 DBI_0.3.1
[19] dichromat_2.0-0 digest_0.6.8 fail_1.2
[22] foreach_1.4.2 foreign_0.8-63 Formula_1.2-0
[25] GenomicAlignments_1.2.2 GenomicFeatures_1.18.3 ggplot2_1.0.0
[28] gtable_0.1.2 Hmisc_3.15-0 iterators_1.0.7
[31] lattice_0.20-30 latticeExtra_0.6-26 MASS_7.3-39
[34] matrixStats_0.14.0 munsell_0.4.2 nnet_7.3-9
[37] plyr_1.8.1 proto_0.3-10 RColorBrewer_1.1-2
[40] Rcpp_0.11.5 RCurl_1.95-4.5 reshape2_1.4.1
[43] rpart_4.1-9 Rsamtools_1.18.3 RSQLite_1.0.0
[46] rtracklayer_1.26.2 scales_0.2.4 sendmailR_1.2-1
[49] splines_3.1.1 stringr_0.6.2 survival_2.38-1
[52] tools_3.1.1 VariantAnnotation_1.12.2 XML_3.98-1.1
[55] zlibbioc_1.12.0