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.
>
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>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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