[R] a suggestion about the display of structural variants in R

[Bogdan Tanasa]

Dear Boris,

good morning, and thank you for your message.  After thinking a bit more
yesterday, I believe that I could adapt the functionality of some R
packages that display the synteny regions across multiple species (here
please see an example Figure 1 from http://www.g3journal.org/
content/7/6/1775.figures-only),

although I have not found yet a R package that does this display (in my
case, instead of distinct species, I will just show distinct chromosomes
connected by translocations). If you have any suggestions, please let me
know.

thanks a lot,

-- bogdan


On Sat, Jul 28, 2018 at 6:42 AM, Boris Steipe <boris.steipe using utoronto.ca>
wrote:

> Maybe the Bioconductor package "intansv" can help you. You asked for
> linear chromosomes, but such data is commonly plotted in Circos plots as
> e.g. with the Bioconductor OmicsCircos package (cf.
> https://bioconductor.org/packages/devel/bioc/vignettes/
> OmicCircos/inst/doc/OmicCircos_vignette.pdf)
>
> However the Bioconductor Project has its own support mailing list, R-Help
> is for programming help.
>
>
> B.
>
>
>
> > On 2018-07-28, at 02:24, Bogdan Tanasa <tanasa using gmail.com> wrote:
> >
> > Dear all,
> >
> > we wish you a fruitful and refreshing weekend ! Thought that I may also
> > write to ask you for a suggestion, specifically if you could please
> advise
> > on whether there is any package already built (in R) that could help with
> > the following data visualization :
> >
> >
> >    we have a set of mutations from many cancer samples
> >
> >    we would like to display the POINT MUTATIONS along the chromosome
> > coordinates (on the linear scale, ie. HORIZONTALLY)
> >
> >    we would like to display the TRANSLOCATIONS (and GENE FUSIONS), as
> > VERTICAL LINES connecting the breakpoints that are located on the
> > chromosomes that are represented HORIZONTALLY
> >
> > Thanks a lot,
> >
> > -- bogdan
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>

	[[alternative HTML version deleted]]