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

[Jeff Newmiller]

My suggestion is to pay attention to Boris and ask people who do this kind 
of plotting frequently... and they are typically found on the Bioconductor 
mailing list, not this list.

On Sat, 28 Jul 2018, Bogdan Tanasa wrote:

> 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]]
>>>
>>> ______________________________________________
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>> posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> 	[[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.
>

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