On Tue, Jan 8, 2013 at 12:20 PM, Tengfei Yin <yintengfei@gmail.com> wrote:

>
>
> On Tue, Jan 8, 2013 at 2:12 PM, Abhishek Pratap <apratap@lbl.gov> wrote:
>
>> Hi Guys
>>
>>
>> I am looking at packages(in(preferred)/out of BioC) that can help me
>> visualize structural variations in our analysis like inter/intra
>> chromosomal translocations, inversions, deletions etc. For now I have
>> looked at Circos which takes some data munging to get a plot ready. I have
>> also glanced at ggbio but dint find an example to visualize intra
>> chromosomal connections which are most interesting to us at this point.
>>
> Hi Abhi,
>
> Have you take a look at the 'circular view' chapter for ggbio's vignette?
>
>
> http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
>
> there is a case study showing how to construct inter/intra chromosomal
> rearrangement as connected lines in circles.
>
> If that is not what you want, would you mind point me to an example
> graphic in Circos, I am glad to add support in ggbio too.
>
> thanks
>
> Tengfei
>

Hi Tengfei

thanks for your quick reply. I think my second msg just crossed yours..:) I
found the example you pointed out.  Let me run through it and try to do the
same with my data.  If I have follow up questions, I will start a new
specific thread.

Cheers!
-Abhi


>
>> Any pointers appreciated.
>>
>>
>> best,
>> -Abhi
>>
>> ------------------------------------
>> Abhishek Pratap
>> Bioinformatics Systems Analyst
>> DOE- Joint Genome Institute
>> Lawrence Berkeley National Lab
>> Walnut Creek, CA
>>
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>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
>
>

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