[Bioc-devel] Why should Bioconductor developers re-use core classes?

Martin Morgan martin.morgan at roswellpark.org
Thu Oct 19 18:15:19 CEST 2017

On 10/19/2017 11:06 AM, Vincent Carey wrote:
> On Thu, Oct 19, 2017 at 10:12 AM, Levi Waldron <lwaldron.research at gmail.com>
> wrote:
>> Thanks for all your thoughts Joey, and I hope I didn't come across as
>> ...
>> On Wed, Oct 18, 2017 at 11:36 PM, Paul Joseph McMurdie <joey711 at gmail.com>
>> wrote:
>> ...
>>> - There actually *still isn't core support for evolutionary trees in
>> BioC* (as
>>> mentioned by Joe Paulson and Ben Callahan in other threads). One of
>>> phyloseq's key contributions was to leverage the fantastic representation
>>> of trees implemented in the CRAN package "ape" in order to support
>> analysis
>>> techniques popular among microbiome researchers that require a
>> phylogenetic
>>> tree. The integration in the phyloseq-class and ape is necessarily pretty
>>> deep, including certain row operations. Users also needed a familiar and
>>> simple R interface to manipulate that composite object despite the
>> complex
>>> hierarchical relationship among rows. Correct me if I'm wrong, but I
>> think
>>> there is still no core BioC support for representing tree-like or
>>> bio-taxonomy-like hierarchy among rows in a SummarizedExperiment, or
>>> equivalent; and consequently certain row operations may have to be
>> modified
>>> more deeply than usual if we were to re-implement phyloseq "the right
>> way".
>>> I'd love to hear thoughts on this.
>> AFAIK you're right, and I don't know the solution, although I hope it can
>> be built on SummarizedExperiment. Looking forward to talking more about
>> this.
> Yes.  Let's write up the use cases and try to spec something out.  Maybe
> start a topic on the support site, or a slack channel?  rowRanges seems
> very useful, perhaps
> a rowGraph/colGraph concept would be useful too.  Establishing idioms for
> using
> these in model specification would be nice.

I started a slack channel for this; all are welcome to participate but I 
don't know how to invite people

I believe people can join the Bioconductor community by visiting



>>> Even though phyloseq is at the receiving end, I think the criticism is
>>> fair, and I want current and future new BioC contributors to not re-make
>> my
>>> mistakes circa 2011-12. I'm happy to help if I can.
>>> Cheers, and thanks for the interesting, collegial thread.
>>> Joey
>> Thanks Joey, and I do want to say also that I think phyloseq is responsible
>> for making Bioconductor a viable and already superior choice for
>> statistical analysis of microbiome data!
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