Michael Lawrence | 11 Jan 01:41 2013

Re: ggbio : misplaced tracks in a test case

On Thu, Jan 10, 2013 at 2:13 PM, Tengfei Yin <yintengfei@...> wrote:

> Hi Abhi,
>
> You raised an important point that users need to pay attention to when they
> construct circular view:
>
> 1. All the data you added on the same circular view, have to have exactly
> the same seqlevels and seqlengths.
> 2. They have to have lengths information for each chromosome, otherwise,
> length is estimated from the data, and it's not accurate in most cases.
>
> it's easy to check when you print the data
> hg19ideo
> test_gr
>
> So in your case, your test_gr's seqlevels is just 1 with seqlengths NA,
> which is not consistency with hg19ideo. So you have to do something similar
> to this
>
> seqlevels(test_gr) <- seqlevels(hg19Ideo)
> seqlengths(test_gr) <- seqlengths(hg19Ideo)
>
>
probably easier to do this all at once with seqinfo<-.

> or do it when you construct the test_gr object.
>
> this will solve the misalignment problem.
>
> HTH
>
> Tengfei
>
> On Thu, Jan 10, 2013 at 4:01 PM, Abhishek Pratap <apratap@...> wrote:
>
> > I am trying to run a test case in ggbio(based on example in a vignette)
> and
> > seem to be running into an odd case where a feature is misplaced on the
> > graph. working Example below
> >
> > In the plot I see the variation(rectangle) is misplaced. I see it on chr3
> > whereas it should be on chr1. plot also attached
> >
> >
> > library(ggbio)
> > data(hg19Ideogram, package = "biovizBase")
> > ## subset_chr
> > chr.sub <- paste("chr", 1:3, sep = "")
> > new.names <- as.character(1:3)
> > names(new.names) <- paste("chr",new.names,sep="")
> > hg19Ideo <- hg19Ideogram
> > hg19Ideo <- keepSeqlevels(hg19Ideogram,chr.sub)
> > hg19Ideo <- renameSeqlevels(hg19Ideo,new.names)
> >
> >
> > p <- ggplot() +
> > layout_circle(hg19Ideo,geom="ideo",fill="gray70",radius=30,trackWidth=4)
> > #adding the scale track
> > p <- p +
> >
> >
> layout_circle(hg19Ideo,geom="scale",fill="gray70",size=4,radius=35,trackWidth=2)
> > #adding the text track
> > p <- p +
> >
> >
> layout_circle(hg19Ideo,geom="text",aes(label=seqnames),vjust=0,radius=39,trackWidth=7,size=6)
> >
> >
> > #testing : placing a rect for a dummy variation
> > test_gr <- GRanges('1',IRanges(start=3000,width=1))
> >
> > #adding the mutant track
> > p <- p +
> >
> layout_circle(test_gr,geom="rect",color="steelblue",radius=23,trackWidth=6)
> > p
> >
> >
> >
> >
> > Thanks!
> > -Abhi
> >
> >
> >
> >
> > > sessionInfo()R version 2.15.2 (2012-10-26)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> > LC_TIME=en_US.UTF-8
> >  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
> > LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=C                 LC_NAME=C
> > LC_ADDRESS=C
> > [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> > LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] biovizBase_1.6.2     rtracklayer_1.18.2   ggbio_1.6.4
> > ggplot2_0.9.3
> > [5] GenomicRanges_1.10.5 IRanges_1.16.3       BiocGenerics_0.4.0
> >
> > _______________________________________________
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> > Search the archives:
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> >
>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
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>
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