Dear all, I would like to represent 2 (chromosomal) interactions as Granges data structure: let's say : chr1 1000-1010 site interacting with chr1 5000-5010 chr1 5000-5010 site interacting with chr1 8000-8010 in order to apply the function geom_arch in ggbio for visualization ... I would appreciate any suggestions in this respect. thanks very much, Bogdan -- output of sessionInfo(): ggplot() + geom_arch(int) -- Sent via the guest posting facility at bioconductor.org.

Hi Bogdan, I replied your email, but I guess I need to reply in the list too. For now, you can only use arches to show links between two point, not two regions, I can put this request in my todo, so in the example, I am just using the midpoint of the interval, if you need further help, e.g show them in circular view as links or build it in tracks with other genomic features, please feel free to send me emails. Thanks a lot Tengfei library(ggbio) ## chr1 1000-1010 site interacting with chr1 5000-5010 ## chr1 5000-5010 site interacting with chr1 8000-8010 library(GenomicRanges) gr <- GRanges("chr1", IRanges(c(1005, 5005), c(5005, 8005))) values(gr)$score <- rnorm(2) gr autoplot(gr, geom = "arch") autoplot(gr, geom = "arch", color = "red") autoplot(gr, geom = "arch", color = "red", aes(height = score)) autoplot(gr, geom = "arch", color = "steelblue", aes(height = score, size = score)) On Tue, Aug 7, 2012 at 12:19 PM, Bogdan Tanasa [guest] < guest@bioconductor.org> wrote: > > Dear all, > > I would like to represent 2 (chromosomal) interactions as Granges data > structure: > > let's say : > chr1 1000-1010 site interacting with chr1 5000-5010 > chr1 5000-5010 site interacting with chr1 8000-8010 > > in order to apply the function geom_arch in ggbio for visualization ... > > I would appreciate any suggestions in this respect. thanks very much, > > Bogdan > > -- output of sessionInfo(): > > ggplot() + geom_arch(int) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 Homepage: www.tengfei.name [[alternative HTML version deleted]]