Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-14 Thread George Vega Yon
Hi Hilmar,

That sounds good. I've actually managed to build rphyloxml very quickly for
creating phyloXML files from phylo (ape) objects.
https://uscbiostats.github.io/rphyloxml/

Perhaps we should continue this discussion outside of the list to see how
can we integrate both packages (no need to have rphyloxml as a package
aside, happy to join RNeXML :))

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

On Thu, Dec 14, 2017 at 4:22 PM, Hilmar Lapp <hilmar.l...@duke.edu> wrote:

> Hi George,
>
> Yes, there’s RNeXML. Glad you found it on your own, I’ve been occupied
> with a workshop. Note that there’s a publication on RNeXML too, as you’ve
> probably seen in the README on Github.
>
> Personally, I think it’d be great to have phyloXML support as well in the
> R ecosystem. However, I’d argue that while the two exchange standards have
> different strengths (and NeXML is not without its own “warts”), for the
> benefit of the user (typically a biology scientist-developer) it would seem
> to be vastly preferable if these standards converge at the R API level. So
> maybe phyloXML support could be added on to RNeXML, or if its own package,
> at least the R API signature could be kept in synchrony?
>
>   -hilmar
>
> > On Dec 14, 2017, at 3:41 PM, George Vega Yon <g.vega...@gmail.com>
> wrote:
> >
> > Hey,
> >
> > Just for the record. I just found two alternatives that seem to be in
> > active development, nexml (www.nexml.org) and RecPhyloXML (
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__
> phylariane.univ-2Dlyon1.fr_recphyloxml_=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=5CdlhUFqJAcw9qGduCmWrGXPwhWFUh
> ZMcOss0uysZ34= ). nexml is supported by
> > rOpenSci (https://urldefense.proofpoint.com/v2/url?u=https-
> 3A__github.com_ropensci_RNeXML=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=E2KdcumsPG-
> JacTs6EbDx9PNds1g15J0lpbZVFgcnLs= ), and both have C++/phython
> > APIs that can be useful for R package development.
> >
> > I still may try to get something done on PhyloXML since jsPhyloSVG, which
> > I'm working on now https://urldefense.proofpoint.com/v2/url?u=https-3A__
> uscbiostats.github.io_jsPhyloSVG_=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=qCOKU5kc59kVmuDmY13hm0h_F0-
> 5VtB-8YC5dp3Nc_I= , only supports
> > annotations in PhyloXML (it does support nexml trees, but I don't think
> it
> > support annotations).
> >
> > Best,
> >
> > George G. Vega Yon
> > +1 (626) 381 8171 <(626)%20381-8171>
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw=
> >
> > On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
> > wrote:
> >
> >> That's a good suggestion. I'll reach out  the rOpenSci people/
> >>
> >> Still, I'm starting a repo here: https://urldefense.proofpoint.
> com/v2/url?u=https-3A__github.com_USCBiostats_rphyloxml=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv-
> IATJ8VuI=
> >> will start dropping stuff there.
> >>
> >> Best,
> >>
> >> George G. Vega Yon
> >> +1 (626) 381 8171 <(626)%20381-8171>
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=
> imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_
> 7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-
> 6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-
> LJHbo4BTkG73yMtknFw=
> >>
> >> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com>
> >> wrote:
> >>
> >>> Sounds like a good idea. Not sure if you’re reinventing the wheel or
> not.
> >>> Sounds like something ROpenSci might support; see:
> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_ropensci_onboarding=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6Y
> HLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_
> Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=Xaz1EafJxnCZMDhwVbMq39-
> DSlGClnlW10wmp8307EA=
> >>>
> >>>
> >>>
> >>>
> 

Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-14 Thread Hilmar Lapp
Hi George,

Yes, there’s RNeXML. Glad you found it on your own, I’ve been occupied with a 
workshop. Note that there’s a publication on RNeXML too, as you’ve probably 
seen in the README on Github.

Personally, I think it’d be great to have phyloXML support as well in the R 
ecosystem. However, I’d argue that while the two exchange standards have 
different strengths (and NeXML is not without its own “warts”), for the benefit 
of the user (typically a biology scientist-developer) it would seem to be 
vastly preferable if these standards converge at the R API level. So maybe 
phyloXML support could be added on to RNeXML, or if its own package, at least 
the R API signature could be kept in synchrony?

  -hilmar

> On Dec 14, 2017, at 3:41 PM, George Vega Yon <g.vega...@gmail.com> wrote:
> 
> Hey,
> 
> Just for the record. I just found two alternatives that seem to be in
> active development, nexml (www.nexml.org) and RecPhyloXML (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__phylariane.univ-2Dlyon1.fr_recphyloxml_=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=5CdlhUFqJAcw9qGduCmWrGXPwhWFUhZMcOss0uysZ34=
>  ). nexml is supported by
> rOpenSci 
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_RNeXML=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=E2KdcumsPG-JacTs6EbDx9PNds1g15J0lpbZVFgcnLs=
>  ), and both have C++/phython
> APIs that can be useful for R package development.
> 
> I still may try to get something done on PhyloXML since jsPhyloSVG, which
> I'm working on now 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uscbiostats.github.io_jsPhyloSVG_=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=qCOKU5kc59kVmuDmY13hm0h_F0-5VtB-8YC5dp3Nc_I=
>  , only supports
> annotations in PhyloXML (it does support nexml trees, but I don't think it
> support annotations).
> 
> Best,
> 
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw=
>  
> 
> On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
> wrote:
> 
>> That's a good suggestion. I'll reach out  the rOpenSci people/
>> 
>> Still, I'm starting a repo here: 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_USCBiostats_rphyloxml=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv-IATJ8VuI=
>>  
>> will start dropping stuff there.
>> 
>> Best,
>> 
>> George G. Vega Yon
>> +1 (626) 381 8171 <(626)%20381-8171>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw=
>>  
>> 
>> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com>
>> wrote:
>> 
>>> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
>>> Sounds like something ROpenSci might support; see:
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_onboarding=DwIGaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I=Xaz1EafJxnCZMDhwVbMq39-DSlGClnlW10wmp8307EA=
>>>  
>>> 
>>> 
>>> 
>>> 
>>> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>>> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>>> Date: December 12, 2017 at 4:13:59 PM
>>> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
>>> <r-sig-phylo@r-project.org>
>>> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>>> 
>>> Hey,
>>> 
>>> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
>>> for visualizing phylogenetic trees on the web browser) in R, and just got
>>> to learn about the phyloXML format. Googling around and checking out this
>>> email list archives it seems that there's no support for this format in
>>> R.
>>> 
>>> My question is: how useful do you think having th

Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-14 Thread George Vega Yon
Hey,

Just for the record. I just found two alternatives that seem to be in
active development, nexml (www.nexml.org) and RecPhyloXML (
http://phylariane.univ-lyon1.fr/recphyloxml/). nexml is supported by
rOpenSci (https://github.com/ropensci/RNeXML), and both have C++/phython
APIs that can be useful for R package development.

I still may try to get something done on PhyloXML since jsPhyloSVG, which
I'm working on now https://uscbiostats.github.io/jsPhyloSVG/, only supports
annotations in PhyloXML (it does support nexml trees, but I don't think it
support annotations).

Best,

George G. Vega Yon
+1 (626) 381 8171 <(626)%20381-8171>
http://ggvy.cl

On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
wrote:

> That's a good suggestion. I'll reach out  the rOpenSci people/
>
> Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml
> will start dropping stuff there.
>
> Best,
>
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> http://ggvy.cl
>
> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com>
> wrote:
>
>> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
>> Sounds like something ROpenSci might support; see:
>> https://github.com/ropensci/onboarding
>>
>>
>>
>>
>> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>> Date: December 12, 2017 at 4:13:59 PM
>> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
>> <r-sig-phylo@r-project.org>
>> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>>
>> Hey,
>>
>> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
>> for visualizing phylogenetic trees on the web browser) in R, and just got
>> to learn about the phyloXML format. Googling around and checking out this
>> email list archives it seems that there's no support for this format in
>> R.
>>
>> My question is: how useful do you think having this in R will be? I'm
>> willing to write an R package to read/write trees in this format (done
>> before with GEXF, which is for networks in general). But I just want to
>> make sure that (1) this will be useful for the community, and (2) I'm not
>> reinventing the wheel (is anybody working on this now?). What are your
>> thoughts?
>>
>> Best,
>>
>> George G. Vega Yon
>> +1 (626) 381 8171 <(626)%20381-8171>
>> http://ggvy.cl
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at http://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>>
>>
>

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Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-13 Thread George Vega Yon
That's a good suggestion. I'll reach out  the rOpenSci people/

Still, I'm starting a repo here: https://github.com/USCBiostats/rphyloxml
will start dropping stuff there.

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop@gmail.com> wrote:

> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
> Sounds like something ROpenSci might support; see:
> https://github.com/ropensci/onboarding
>
>
>
>
> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
> Date: December 12, 2017 at 4:13:59 PM
> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
> <r-sig-phylo@r-project.org>
> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>
> Hey,
>
> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
> for visualizing phylogenetic trees on the web browser) in R, and just got
> to learn about the phyloXML format. Googling around and checking out this
> email list archives it seems that there's no support for this format in R.
>
> My question is: how useful do you think having this in R will be? I'm
> willing to write an R package to read/write trees in this format (done
> before with GEXF, which is for networks in general). But I just want to
> make sure that (1) this will be useful for the community, and (2) I'm not
> reinventing the wheel (is anybody working on this now?). What are your
> thoughts?
>
> Best,
>
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> http://ggvy.cl
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>
>

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] Will phyloXML in R be useful?

2017-12-12 Thread Daniel Fulop
Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
Sounds like something ROpenSci might support; see:
https://github.com/ropensci/onboarding




From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
Date: December 12, 2017 at 4:13:59 PM
To: Group R-sig-phylo <r-sig-phylo@r-project.org>
<r-sig-phylo@r-project.org>
Subject:  [R-sig-phylo] Will phyloXML in R be useful?

Hey,

Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
for visualizing phylogenetic trees on the web browser) in R, and just got
to learn about the phyloXML format. Googling around and checking out this
email list archives it seems that there's no support for this format in R.

My question is: how useful do you think having this in R will be? I'm
willing to write an R package to read/write trees in this format (done
before with GEXF, which is for networks in general). But I just want to
make sure that (1) this will be useful for the community, and (2) I'm not
reinventing the wheel (is anybody working on this now?). What are your
thoughts?

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

[[alternative HTML version deleted]]

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[R-sig-phylo] Will phyloXML in R be useful?

2017-12-12 Thread George Vega Yon
Hey,

Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
for visualizing phylogenetic trees on the web browser) in R, and just got
to learn about the phyloXML format. Googling around and checking out this
email list archives it seems that there's no support for this format in R.

My question is: how useful do you think having this in R will be? I'm
willing to write an R package to read/write trees in this format (done
before with GEXF, which is for networks in general). But I just want to
make sure that (1) this will be useful for the community, and (2) I'm not
reinventing the wheel (is anybody working on this now?). What are your
thoughts?

Best,

George G. Vega Yon
+1 (626) 381 8171
http://ggvy.cl

[[alternative HTML version deleted]]

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