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

Bhagwat, Aditya Ad|ty@@Bh@gw@t @end|ng |rom mp|-bn@mpg@de
Thu Sep 12 13:00:41 CEST 2019 

Thankyou Bernat!

-----Original Message-----
From: Bernat Gel Moreno <bgel using igtp.cat> 
Sent: Donnerstag, 12. September 2019 11:26
To: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

I have updated karyoploteR and it's now (from version 1.11.9 in devel) possible to use a BSgenome object or a seqinfo object as genome definitions in plotKaryotype. In both cases, if possible, it will by default automatically filter the chromosomes to the canonical ones (if
defined) and retrieve the cytobands for the genome. Or you can specify the exact chromosomes you want to plot. I think this should help with the specific question at hand.

Bernat


El 9/12/19 a las 10:09 AM, Bernat Gel Moreno escribió:
> 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.bioc
>>>>> onductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>B
>>>>> Sgenome (without the _random or _unassigned), but Lori explained 
>>>>> this is not possible.
>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioc
>>>>> onductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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.bioc
>>>>> onductor.org_p_123489&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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.bioc
>>>>> onductor.org_p_124416&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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.bioc
>>>>> onductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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.bioc
>>>>> onductor.org_p_124328&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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.bioc
>>>>> onductor.org_p_124491&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK
>>>>> 7PEM0aanQY4M6wY&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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