[Bioc-devel] Extending biovizBase and ggbio packages

[Michael Lawrence]

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 at 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 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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