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

Boris Steipe bor|@@@te|pe @end|ng |rom utoronto@c@
Sat Jul 28 15:42:59 CEST 2018

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.


> 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]]
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