Abhishek Pratap | 11 Jan 01:59 2013

Re: ggbio : misplaced tracks in a test case

thanks guys. that worked fine.

In future may be this check could be implicit in the layout_circle method
which could complain if the seqinfo doesnt match. I guess it would avoid
some clueless moments for new users of ggbio like me :).

Cheers!
-Abhi

On Thu, Jan 10, 2013 at 4:41 PM, Michael Lawrence <lawrence.michael@...
> wrote:

>
>
>
> 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
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
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>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>>
>>
>>
>> --
>> Tengfei Yin
>> MCDB PhD student
>> 1620 Howe Hall, 2274,
>> Iowa State University
>> Ames, IA,50011-2274
>>
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>>
>>
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>
>

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