[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Bernat Gel Moreno bge| @end|ng |rom |gtp@c@t
Thu Sep 12 10:09:30 CEST 2019 

Oh, and Aditya, take into account taht if you give karyoploteR a custom 
genome as you are planning to do, it will not paint the cytobands by 
default, you'll have to get them yourself and give them to plotKaryotype.

If possible, I would recommend giving the genome by name ("hg19") and 
selecting the chromosomes to plot using "chromosomes".

Bernat




El 9/12/19 a las 8:47 AM, Bernat Gel Moreno escribió:
> Hi all,
>
> I'm the developer of karyoploteR.
>
> @Michael: I never though about using seqinfo as the source for the
> genome information. I'll add this as an option to define the genome.
> Thanks for the suggestion.
>
> @Aditya: If you want to plot just your relevant chromosomes, you don't
> need to alter the genome. You can use the "chromosomes" parameter to
> give a vector of chromosome names. Is it not working for you for some
> reason?
>
> Bernat
>
>
> El 9/11/19 a las 2:31 PM, Michael Lawrence via Bioc-devel escribió:
>> I'm pretty surprised that the karyoploteR package does not accept a
>> Seqinfo since it is plotting chromosomes. But again, please consider
>> just doing as(seqinfo(bsgenome), "GRanges").
>>
>> On Wed, Sep 11, 2019 at 3:59 AM Bhagwat, Aditya
>> <Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
>>> Hi Herve,
>>>
>>> Thank you for your responses.
>>>   From your response, it is clear that the vcountPDict use case does not need a BSgenome -> GRanges coercer.
>>>
>>> The karyoploteR use case still requires it, though, to allow plotting of only the chromosomal BSgenome portions:
>>>
>>>       chromranges <- as(bsegenome, "GRanges")
>>>       kp <- karyoploteR::plotKaryotype(chromranges)
>>>       karyoploteR::kpPlotRegions(kp, crispr_target_sites)
>>>
>>> Or do you see any alternative for this purpose too?
>>>
>>> Aditya
>>>
>>> ________________________________________
>>> From: Pages, Herve [hpages using fredhutch.org]
>>> Sent: Wednesday, September 11, 2019 12:24 PM
>>> To: Bhagwat, Aditya; bioc-devel using r-project.org
>>> Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?
>>>
>>> Hi Aditya,
>>>
>>> On 9/11/19 01:31, Bhagwat, Aditya wrote:
>>>> Hi Herve,
>>>>
>>>>
>>>>    > It feels that a coercion method from BSgenome to GRanges should
>>>> rather be defined in the BSgenome package itself.
>>>>
>>>> :-)
>>>>
>>>>
>>>>    > Patch/PR welcome on GitHub.
>>>>
>>>> Owkies. What pull/fork/check/branch protocol to be followed?
>>>>
>>>>
>>>>    > Is this what you have in mind for this coercion?
>>>>    > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
>>>>
>>>> Yes.
>>>>
>>>> Perhaps also useful to share the wider context, allowing your and others
>>>> feedback for improved software design.
>>>> I wanted to subset a
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>BSgenome
>>>> (without the _random or _unassigned), but Lori explained this is not
>>>> possible.
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>
>>>>
>>>> Instead Lori suggested to coerce a BSgenome into a GRanges
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123489&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=6Eh73QthFfpPsfpRdPWs98pH6GHvv1Z23ORp34OCPxA&e=>,
>>>> which is a useful solution, but for which currently no exported S4
>>>> method exists
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124416&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=H8owJlOQrNHwNFHfCxGHe27Jxu6xjxpuAMWK8JlTU4Y&e=>
>>>> So I defined an S4 coercer in my multicrispr package, making sure to
>>>> properly import the Bsgenome class
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=2XNBVcwoJTjlxY_gl4UPzrHPKmKH9LTnM4ih5SQOfps&e=>.
>>>> Then, after coercing a BSgenome into a GRanges, I can extract the
>>>> chromosomes, after properly importing IRanges::`%in%`
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>
>>> Looks like you don't need to coerce the BSgenome object to GRanges. See
>>> https://support.bioconductor.org/p/123489/#124581
>>>
>>> H.
>>>
>>>> Which I can then on end to karyoploteR
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124328&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=M90_rBO1oohGnXe2XBpQHQriFNthY_W0hzN6KWlf2S4&e=>,
>>>> for genome-wide plots of crispr target sites.
>>>>
>>>> A good moment also to say thank you to all of you who helped me out, it
>>>> helps me to make multicrispr fit nicely into the BioC ecosystem.
>>>>
>>>> Speeking of BioC design philosophy, can any of you suggest concise and
>>>> to-the-point reading material to deepen my understanding of the core
>>>> BioC software design philosophy?
>>>> I am trying to understand that better (which was the context for asking
>>>> recently why there are three Vector -> data.frame coercers in S4Vectors
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124491&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=nBHdQoTrd1Mfu4VTMgtkPyUQ0Ju2NLeX-0X1Ny3fSeg&e=>)
>>>>
>>>> Cheers,
>>>>
>>>> Aditya
>>>>
>>>>
>>>>
>>>>
>>>> ________________________________________
>>>> From: Pages, Herve [hpages using fredhutch.org]
>>>> Sent: Tuesday, September 10, 2019 6:45 PM
>>>> To: Bhagwat, Aditya; bioc-devel using r-project.org
>>>> Subject: Re: [Bioc-devel] Import BSgenome class without attaching
>>>> BiocGenerics (and others)?
>>>>
>>>> Hi Aditya,
>>>>
>>>>
>>>> More generally speaking, coercion methods should be defined in a place
>>>> that is "as close as possible" to the "from" or "to" classes rather than
>>>> in a package that doesn't own any of the 2 classes involved.
>>>> Is this what you have in mind for this coercion?
>>>>
>>>>    > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
>>>> GRanges object with 7 ranges and 0 metadata columns:
>>>> seqnames ranges strand
>>>> <Rle> <IRanges> <Rle>
>>>> chrI chrI 1-15072423 *
>>>> chrII chrII 1-15279345 *
>>>> chrIII chrIII 1-13783700 *
>>>> chrIV chrIV 1-17493793 *
>>>> chrV chrV 1-20924149 *
>>>> chrX chrX 1-17718866 *
>>>> chrM chrM 1-13794 *
>>>> -------
>>>> seqinfo: 7 sequences (1 circular) from ce10 genome
>>>>
>>>> Thanks,
>>>> H.
>>>>
>>>>
>>>> On 9/6/19 03:39, Bhagwat, Aditya wrote:
>>>>    > Dear Bioc devel,
>>>>    >
>>>>    > Is it possible to import the BSgenome class without attaching
>>>> BiocGenerics (to keep a clean namespace during the development of
>>>> multicrispr<https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.gwdg.de_loosolab_software_multicrispr&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=MIR-kUeXy9oWokdQxItuG82hrvs0uwP1aBIqNdM-Jrs&e=
>>>>    >).
>>>>    >
>>>>    > BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
>>>>    >
>>>>    > (Posted earlier on BioC
>>>> support<https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=oBSScH5uD5j0vCAaj4dfWepjiNGtHm9q5gA8eaIudZ4&e=
>>>>    > and redirected here following Martin's suggestion)
>>>>    >
>>>>    > Thankyou :-)
>>>>    >
>>>>    > Aditya
>>>>    >
>>>>    > [[alternative HTML version deleted]]
>>>>    >
>>>>    > _______________________________________________
>>>>    > Bioc-devel using r-project.org mailing list
>>>>    >
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=cEojiObibdSuzmh21opvy85DZyRrjtfo1vEMopKWmAg&e=
>>>>    >
>>>>
>>>> --
>>>> Hervé Pagès
>>>>
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M1-B514
>>>> P.O. Box 19024
>>>> Seattle, WA 98109-1024
>>>>
>>>> E-mail: hpages using fredhutch.org
>>>> Phone: (206) 667-5791
>>>> Fax: (206) 667-1319
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages using fredhutch.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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