[Bioc-devel] Extending biovizBase and ggbio packages

[Michael Lawrence]

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 at 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 at eurac.edu> wrote:
>
> I’ll do, thanks for all comments!
>
>
> On 14 Dec 2015, at 15:55, Jim Hester <james.f.hester at 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 at 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 at 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 at 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 at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
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>
>
>
>