[BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Robert Ivanek
robert.ivanek at unibas.ch
Wed Jul 17 12:29:05 CEST 2013
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
>
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