a suggestion about the display of structural variants in R

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a suggestion about the display of structural variants in R

Bogdan Tanasa
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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Re: a suggestion about the display of structural variants in R

Boris Steipe
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 <[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: 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 <[hidden email]>
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 <[hidden email]> 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]]
> >
> > ______________________________________________
> > [hidden email] 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]]

______________________________________________
[hidden email] 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
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Re: 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 <[hidden email]>
> 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 <[hidden email]> 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]]
>>>
>>> ______________________________________________
>>> [hidden email] 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]]
>
> ______________________________________________
> [hidden email] 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.
>

---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
                                       Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k

______________________________________________
[hidden email] 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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Re: 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 <[hidden email]>
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 <[hidden email]>
>> 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 <[hidden email]> 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]]
>>>>
>>>> ______________________________________________
>>>> [hidden email] 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]]
>>
>> ______________________________________________
>> [hidden email] 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.
>>
>>
> ------------------------------------------------------------
> ---------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ------------------------------------------------------------
> ---------------
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.