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 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> 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 > > > [[alternative HTML version deleted]]