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.bhag...@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 [hpa...@fredhutch.org] >>> Sent: Wednesday, September 11, 2019 12:24 PM >>> To: Bhagwat, Aditya; bioc-devel@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 [hpa...@fredhutch.org] >>>> Sent: Tuesday, September 10, 2019 6:45 PM >>>> To: Bhagwat, Aditya; bioc-devel@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@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: hpa...@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: hpa...@fredhutch.org >>> Phone: (206) 667-5791 >>> Fax: (206) 667-1319 >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel