[Bioc-devel] Extending biovizBase and ggbio packages

[Rainer Johannes]

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 at 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 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
>>> 
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
>>