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ggbio facet_gr example sought

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Malcolm Cook ★ 1.6k

@malcolm-cook-6293

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Hi, I am unable to find any examples of facet_gr argument to autoplot. It is mentioned in http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio.pdf on page 9 as: Sometime, we need to view different regions, so we also have a facet_gr argument which accept a GRanges. If this is provided, it will override the default seqnames and use provided region to facet the graphics, this might be useful for different gene centric views. However there is no further example of its use, and it does not appear in the list of formals, and it does not appear at all in http://biocon ductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ggbio.pdf And the only google hits suggest this feature is out deprecated. Am I missing something? Is there a contemporary equivalent? Is there some way to facet on genomic range? Any examples out there? Thanks, ~ malcolm_cook@stowers.org [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.3 years ago by Michael Lawrence ★ 11k • written 11.3 years ago by Malcolm Cook ★ 1.6k

score 0 · Answer 1 · 2013-08-06

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

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I'm pretty sure that you can just pass a GRanges to the facets argument, but I haven't tried it. On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec@stowers.org> wrote: > Hi, > I am unable to find any examples of facet_gr argument to autoplot. > > It is mentioned in > http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio.pdf on > page 9 as: > > Sometime, we need to view different regions, so we also have a facet_gr > argument which > accept a GRanges. If this is provided, it will override the default > seqnames and use provided > region to facet the graphics, this might be useful for different gene > centric views. > > > However there is no further example of its use, and it does not appear in > the list of formals, and it does not appear at all in > http://bioconductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ ggbio.pdf > > And the only google hits suggest this feature is out deprecated. > > Am I missing something? > > Is there a contemporary equivalent? Is there some way to facet on > genomic range? Any examples out there? > > Thanks, > > ~ malcolm_cook@stowers.org > [[alternative HTML version deleted]]

ADD COMMENT • link 11.3 years ago Michael Lawrence ★ 11k

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Hi Michael and Malcolm, Sorry for the late reply, that's actually a bug in ggbio now. I did deprecate facet_gr() function, but the feature is kept, it is supposed (used) to work when you pass GRanges to arguments 'facets', either in autoplot() or the low level API. Some of my updates broke this feature. Thanks for pointing this out. I will work on fixing this bug. Tengfei Tengfei On Tue, Aug 6, 2013 at 4:13 PM, Michael Lawrence <lawrence.michael@gene.com>wrote: > I'm pretty sure that you can just pass a GRanges to the facets argument, > but I haven't tried it. > > > On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec@stowers.org> wrote: > >> Hi, >> I am unable to find any examples of facet_gr argument to autoplot. >> >> It is mentioned in >> http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio. pdfon page 9 as: >> >> Sometime, we need to view different regions, so we also have a facet_gr >> argument which >> accept a GRanges. If this is provided, it will override the default >> seqnames and use provided >> region to facet the graphics, this might be useful for different gene >> centric views. >> >> >> However there is no further example of its use, and it does not appear >> in the list of formals, and it does not appear at all in >> http://bioconductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc /ggbio.pdf >> >> And the only google hits suggest this feature is out deprecated. >> >> Am I missing something? >> >> Is there a contemporary equivalent? Is there some way to facet on >> genomic range? Any examples out there? >> >> Thanks, >> >> ~ malcolm_cook@stowers.org >> > > [[alternative HTML version deleted]]

ADD REPLY • link 11.3 years ago Tengfei Yin ▴ 420

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Tengfei, Thanks for acknowledging this issue. I played around with this for a while more after Michael's comment, but could find no syntax that did not generate an error. I look forward to learning about this capability once you have it working as you intend. Cheers, ~ malcolm_cook@stowers.org ________________________________ From: Tengfei Yin [yintengfei@gmail.com] Sent: Tuesday, August 06, 2013 10:17 PM To: Michael Lawrence Cc: Cook, Malcolm; bioconductor@r-project.org Subject: Re: ggbio facet_gr example sought Hi Michael and Malcolm, Sorry for the late reply, that's actually a bug in ggbio now. I did deprecate facet_gr() function, but the feature is kept, it is supposed (used) to work when you pass GRanges to arguments 'facets', either in autoplot() or the low level API. Some of my updates broke this feature. Thanks for pointing this out. I will work on fixing this bug. Tengfei Tengfei On Tue, Aug 6, 2013 at 4:13 PM, Michael Lawrence <lawrence.michael@gene.com<mailto:lawrence.michael@gene.com>> wrote: I'm pretty sure that you can just pass a GRanges to the facets argument, but I haven't tried it. On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec@stowers.org<mailto:mec@stowers.org>> wrote: Hi, I am unable to find any examples of facet_gr argument to autoplot. It is mentioned in http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio.pdf on page 9 as: Sometime, we need to view different regions, so we also have a facet_gr argument which accept a GRanges. If this is provided, it will override the default seqnames and use provided region to facet the graphics, this might be useful for different gene centric views. However there is no further example of its use, and it does not appear in the list of formals, and it does not appear at all in http://biocon ductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ggbio.pdf And the only google hits suggest this feature is out deprecated. Am I missing something? Is there a contemporary equivalent? Is there some way to facet on genomic range? Any examples out there? Thanks, ~ malcolm_cook@stowers.org<mailto:malcolm_cook@stowers.org> [[alternative HTML version deleted]]

ADD REPLY • link 11.3 years ago Malcolm Cook ★ 1.6k