R help - Jul 2018 - a suggestion about the display of structural variants in R

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

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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 at 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 at 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.

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 at
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 at 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 at 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.
>
>
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