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

[Bogdan Tanasa]

Thank you Jeff. Yes, certainly, I posted a message on BioC too, although I
have not received any suggestions by now.

On Sat, Jul 28, 2018 at 8:05 AM, Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> 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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>>>> 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]]
>>
>> ______________________________________________
>> 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/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
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