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Question: Gviz: Use of transcriptAnnotation in BiomartGeneRegionTrack
0
gravatar for broder.engler
3.7 years ago by
Germany
broder.engler0 wrote:

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         

 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by broder.engler0
0
gravatar for florian.hahne@novartis.com
3.7 years ago by
Switzerland

Hi Broder,

the problem here is that you asked for stacking="dense". This causes all the features of your gene model to be condensed into a single line. Because there are overlapping items and the reult of this is some sort of meta-transcript, there is no meaningful way to add transcript labels anymore. You will see the gene symbols as expected when plotting with stacking="squish", or when creating the BiomartGeneRegionTrack without the stacking option

plotTracks(bmt, from=afrom, to=ato, chromosome=chr, transcriptAnnotation="symbol", stacking="squish")

Florian

 
ADD COMMENTlink written 3.7 years ago by florian.hahne@novartis.com1.6k
0
gravatar for broder.engler
3.7 years ago by
Germany
broder.engler0 wrote:

Hi Florian,

Now it works like a charm! Thanks a lot!

Best,
Broder

ADD COMMENTlink written 3.7 years ago by broder.engler0
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