Tengfei Yin | 11 Jan 02:10 2013
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Re: ggbio : misplaced tracks in a test case

On Thu, Jan 10, 2013 at 6:59 PM, Abhishek Pratap <apratap@...> wrote:

> 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 :).
>

right, I have been thinking about an better way for automatic checking of
seqinfo or doing something like you suggested, and will probably
implemented that feature in next release. Thanks for your suggestions.

Tengfei

>
> 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
>>> >
>>> > _______________________________________________
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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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>>
>>
>

--

-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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