[Bioc-devel] Extending biovizBase and ggbio packages

[Rainer Johannes]

I’ll do, thanks for all comments!


On 14 Dec 2015, at 15:55, Jim Hester <james.f.hester at gmail.com<mailto: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<mailto: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<mailto: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<mailto: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
>> _______________________________________________
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