'Re: [Bioc-devel] Extending biovizBase and ggbio packages'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] Extending biovizBase and ggbio packages
From:       Michael Lawrence <lawrence.michael () gene ! com>
Date:       2015-12-16 18:12:52
Message-ID: CAOQ5Nyc9J=0aLgxJB25i7m-P9xTNOKf5ooJMhBLz+Fs0LAeTbw () mail ! gmail ! com
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Awesome. That's great (and fast) work. I will add you to the author
list of both packages.

Thanks a lot for your contribution,
Michael

On Wed, Dec 16, 2015 at 6:15 AM, Rainer Johannes
<Johannes.Rainer@eurac.edu> wrote:
> OK, I have cleared the code duplications and pushed to my biovizBase and ggbio \
> forks. Also, in the crunch method for EnsDb I'm avoiding now the loops. Thanks \
> Michael! 
> jo
> 
> > On 15 Dec 2015, at 15:43, Rainer Johannes <Johannes.Rainer@eurac.edu> wrote:
> > 
> > Thanks for the comments! I'll make some changes and push a "cleaner" version once \
> > I'm done. Indeed, I have to reduce code duplications. I could also use the same \
> > or similar code than for TxDb, but I wanted to make as much use of the EnsDb \
> > filter system as possible to reduce processing time. 
> > jo
> > 
> > 
> > > On 15 Dec 2015, at 15:00, Michael Lawrence <lawrence.michael@gene.com> wrote:
> > > 
> > > Great, thanks for this valuable contribution. I made some comments on
> > > the commits. The biggest issue is that I think there is a lot of code
> > > duplication between the EnsDb and TxDb methods. We should try hard to
> > > reduce this.
> > > 
> > > Michael
> > > 
> > > On Tue, Dec 15, 2015 at 1:37 AM, Rainer Johannes
> > > <Johannes.Rainer@eurac.edu> wrote:
> > > > OK, the modifications are in the repositories:
> > > > https://github.com/jotsetung/biovizBase
> > > > https://github.com/jotsetung/ggbio
> > > > 
> > > > let me know if I can be of any help.
> > > > 
> > > > cheers, jo
> > > > 
> > > > 
> > > > 
> > > > On 14 Dec 2015, at 16:00, Rainer Johannes <Johannes.Rainer@eurac.edu> wrote:
> > > > 
> > > > I'll do, thanks for all comments!
> > > > 
> > > > 
> > > > On 14 Dec 2015, at 15:55, Jim Hester <james.f.hester@gmail.com> wrote:
> > > > 
> > > > Rainer,
> > > > 
> > > > Pull requests to the git mirrors will be closed automatically because they
> > > > are read only mirrors. However you can still fork the mirror yourself and
> > > > commit your changes to your fork to make them easy for Michael and Tengfei
> > > > to review.
> > > > 
> > > > Jim
> > > > 
> > > > On Mon, Dec 14, 2015 at 9:03 AM, Rainer Johannes <Johannes.Rainer@eurac.edu>
> > > > wrote:
> > > > > 
> > > > > dear Micheal,
> > > > > 
> > > > > github pull requests would also be my favorite way to contribute, but
> > > > > unfortunately the Bioconductor-mirror github repos are read-only (thus, as
> > > > > far as I got it, no pull requests are possible), and I didn't find other
> > > > > repos in github.
> > > > > 
> > > > > Regarding the filtering, you mean implementing subset() and sort() in
> > > > > ensembldb?
> > > > > My only concern with the approach you describe below is that it rather
> > > > > looks like "fetch from db and then filter", which might be quite slow. I
> > > > > implemented the filters such that they are considered at query execution
> > > > > time (in fact, they are used to build the SQL query).
> > > > > That way also plotting of gene models in ggbio using EnsDbs is really fast
> > > > > (since only that small portion that will be plotted is really fetched from
> > > > > the db).
> > > > > 
> > > > > thanks, jo
> > > > > 
> > > > > > On 14 Dec 2015, at 14:46, Michael Lawrence <lawrence.michael@gene.com>
> > > > > > wrote:
> > > > > > 
> > > > > > Sounds very useful. Perhaps you could make a github pull request on
> > > > > > the Bioconductor mirrors of those packages. Then Tengfei or I could
> > > > > > look it over.
> > > > > > 
> > > > > > Btw, I like the filtering functionality in ensemldb. Would be nice to
> > > > > > have something as rich for TxDb. Would be great if there were
> > > > > > convenience wrappers like subset() and sort(). Like
> > > > > > transcripts(sort(subset(db, seqname == "chr1"), by = geneSymbol)).
> > > > > > 
> > > > > > Thanks,
> > > > > > Michael
> > > > > > 
> > > > > > On Mon, Dec 14, 2015 at 4:12 AM, Rainer Johannes
> > > > > > <Johannes.Rainer@eurac.edu> wrote:
> > > > > > > Dear all,
> > > > > > > 
> > > > > > > I've modified the biovizBase and ggbio packages so that they do
> > > > > > > directly support EnsDb annotations (just like annotations provided by \
> > > > > > > TxDb objects/packages).
> > > > > > > Is there a way I could provide these changes? I've directly contacted
> > > > > > > Tengfei last week, but did not get any reply yet…
> > > > > > > 
> > > > > > > cheers, jo
> > > > > > > _______________________________________________
> > > > > > > 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
> > > > 
> > > > 
> > > > 
> > > > 
> > 
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> 

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