[Bioc-devel] Extending biovizBase and ggbio packages

[Rainer Johannes]

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 at 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 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
>>> 
>>> 
>>> 
>>> 
> 
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