Question: Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
1
gravatar for Martin Rijlaarsdam
5.6 years ago by
Martin Rijlaarsdam190 wrote:
Dear Robert, Thanks a lot for your reply. I implemented your suggestions and with one additional step it works perfectly now. Apart from setting the chromosome identifier in the ranges from 2 to chr2, the active chromosome for the bmTrack also needs to be set to chr2 after retrieving the data from e! using chromosome(bmTrack)=sprintf("chr%s", chro) Thanks again. Kind regards, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Wed, Jul 17, 2013 at 12:29 PM, Robert Ivanek <robert.ivanek@unibas.ch>wrote: > Dear Martin, > > You are trying to visualize data from two different sources which are > using different chromosome names: > * BiomartGeneRegionTrack based on e! which is using 1, 2, 3, ... X > * IdeogramTrack based on UCSC which is using chr1, chr2, chr3, ... chrX > > You can combine both tracks together in the following way: > > library(Gviz) > ## suppport non-UCSC chromosome names > options(ucscChromosomeNames=FALSE) > ##regions with genes > st=17740000 > ed=17750000 > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > chromosome="chrX", > genome="hg19",showId = > TRUE,background.title = "white", > name="",fontsize=20,col="black") > ## fix the seqlevels (e! is using 1,2, 3 ... X; UCSC is using chr1, > chr2... chrX) > library(GenomicRanges) ## we need function "seqlevels<-" > seqlevels(ranges(bmTrack)) <- sprintf("chr%s", seqlevels(ranges(bmTrack))) > ##empty area > st=20000 > ed=30000 > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > chromosome="chrX", > genome="hg19",showId = > TRUE,background.title = "white", > name="",fontsize=20,col="black") > ## fix the seqlevels (e! is using 1,2, 3 ... X; UCSC is using chr1, > chr2... chrX) > seqlevels(ranges(bmTrack)) <- sprintf("chr%s", seqlevels(ranges(bmTrack))) > ## IdeogramTrack based on UCSC > itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) > gtrack <- GenomeAxisTrack(fontsize=20) > st <- c(st) > ed <- c(ed) > strand <- c("*") > gr <- c("ROI") > annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, > chromosome="chrX", genome="hg19", > feature="ROI", > group=gr, id=paste("test"), name="generic > annotation", stacking="squish", > background.title = > > "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") > plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) > > > Best > Robert > > > On 16/07/13 14:06, Martin Rijlaarsdam wrote: > > Hi, > > > > I am trying to use Gviz to retrieve info from specific regions on the > > genome using the BiomartGeneRegionTrack function. This goes fine with > > all chromosomes except X (and possibly Y, have not been able to test > > that). When I retrieve data for an empty region (20000-30000) all goes > > fine, but in a region with genes (17740000-17750000) the following > > error occurs: > > > > Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x' > > Please consider setting options(ucscChromosomeNames=FALSE) to allow > > for arbitrary chromosome identifiers. > > > > Setting options(ucscChromosomeNames=FALSE) as also described at > > https://stat.ethz.ch/pipermail/bioconductor/2013-April/052153.html > > completely breaks the code (nothing retrieved for any chromosome > > anymore). Moreover, I think I am using the correct identifier: "chrX" > > . Of interest, the ideogram and annotation track are generated fine > > with ' chromosome = "chrX" ' > > > > Thanks a lot for any help! > > > > Best, > > Martin > > > > Sample code: > > > > library(Gviz) > > #regions with genes > > st=17740000 > > ed=17750000 > > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > > chromosome="chrX", > > genome="hg19",showId = TRUE,background.title = "white", > > name="",fontsize=20,col="black") > > #empty area > > st=20000 > > ed=30000 > > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > > chromosome="chrX", > > genome="hg19",showId = TRUE,background.title = "white", > > name="",fontsize=20,col="black") > > itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) > > gtrack <- GenomeAxisTrack(fontsize=20) > > st <- c(st) > > ed <- c(ed) > > strand <- c("*") > > gr <- c("ROI") > > annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, > > chromosome="chrX", genome="hg19", feature="ROI", > > group=gr, id=paste("test"), name="generic annotation", > stacking="squish", > > background.title = > > "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") > > plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) > > > > ---- > > > > output of sessionInfo() > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] grid parallel stats graphics grDevices utils > > datasets methods base > > > > other attached packages: > > [1] Gviz_1.4.4 lumi_2.12.0 Biobase_2.20.0 > BiocGenerics_0.6.0 > > > > loaded via a namespace (and not attached): > > [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 > > AnnotationDbi_1.22.6 > > [5] beanplot_1.1 BiocInstaller_1.10.2 biomaRt_2.16.0 > > Biostrings_2.28.0 > > [9] biovizBase_1.8.1 bitops_1.0-5 BSgenome_1.28.0 > > cluster_1.14.4 > > [13] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 > > GenomicFeatures_1.12.2 > > [17] GenomicRanges_1.12.4 Hmisc_3.12-2 illuminaio_0.2.0 > > IRanges_1.18.2 > > [21] KernSmooth_2.23-10 labeling_0.2 lattice_0.20-15 > > limma_3.16.6 > > [25] MASS_7.3-27 Matrix_1.0-12 matrixStats_0.8.1 > > mclust_4.1 > > [29] methylumi_2.6.1 mgcv_1.7-24 minfi_1.6.0 > > multtest_2.16.0 > > [33] munsell_0.4.2 nleqslv_2.0 nlme_3.1-110 > > nor1mix_1.1-4 > > [37] plyr_1.8 preprocessCore_1.22.0 R.methodsS3_1.4.4 > > RColorBrewer_1.0-5 > > [41] RCurl_1.95-4.1 reshape_0.8.4 rpart_4.1-1 > > Rsamtools_1.12.3 > > [45] RSQLite_0.11.4 rtracklayer_1.20.4 scales_0.2.3 > > siggenes_1.34.0 > > [49] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 > > survival_2.37-4 > > [53] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 > > zlibbioc_1.6.0 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]
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