Hi Bogdan,

You could try package GenomeGraph which pull data from Biomart to create
annotation tracks inside R.

If you are familiar with core Bioc object like GRanges/TranscriptDb, you
can try package ggio, you need to construct your data as GRanges and bundle
them by tracks() function. or grid.arrange() in gridExtra package. ggbio is
a new package, let me know if you come across any problem or you want to
request a new feature.

Or you can fire your data into UCSC genome browser inside R, check
browserGenome function in package rtracklayer.

Interaction between locus is tricky, I don't know about other packages(if
there is any, please let me know, thanks), it could be represented as links
in circular view,  or links in a grand linear view, which is currently
still under development in ggbio and visnab, I will keep you post it, if
you would like to test some functionality.

cheers

Tengfei

On Wed, Nov 9, 2011 at 11:30 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:

> Dear all,
>
> I would appreciate if you can recommend any BioC package where I can
> display togheter a set of features/annotations (eg genes, TF binding
> sites), and 3C interactions data (the 3C chromosomal interactions will be
> represented as lines between interaction loci, or just simply as dots that
> count for an interaction strength at a particular position). thanks,
>
> bogdan
>
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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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