[Bioc-devel] recalling methods
Leonardo Collado Torres
lcollado at jhu.edu
Mon Apr 6 20:31:36 CEST 2015
Somewhat related to this topic, some folks made this package:
https://github.com/hilaryparker/explainr It could be related to
Wolfgang's idea of "learning" which methods are more important, its
just that people would have to write the explanation. Then a new user
can "learn" about it.
On Mon, Apr 6, 2015 at 11:08 AM, Michael Love
<michaelisaiahlove at gmail.com> wrote:
> I just noticed in the newsletter [1] that Martin fixed this in R-devel / R
> 3.2
>
>> methods(class="GenomicRanges")
> [1] != [ [<- %in%
> <
> ...
>
> thanks Martin!
>
> [1]
> http://www.bioconductor.org/help/newsletters/2015_April/#new-and-noteworthy
>
> On Sat, Dec 6, 2014 at 5:32 PM, Michael Lawrence <lawrence.michael at gene.com>
> wrote:
>
>>
>>
>> On Sat, Dec 6, 2014 at 9:23 AM, Wolfgang Huber <whuber at embl.de> wrote:
>>
>>>
>>> Also some interest on our side to contribute.
>>> Perhaps in particular the rendering a useful index (or graph) of man
>>> pages on the fly in HTML / graphically.
>>>
>>>
>> Great, that's the sort of thing I had in mind.
>>
>>
>>> Is it too ambitious to “learn” which methods are most important for
>>> objects of a particular class from analysing (running) a large code base
>>> (or even injecting a hook to that effect into a user’s R)?
>>>
>>>
>> It's a good idea and one that Eclipse and other IDEs use for
>> auto-completion. We'd just have to find the right codebase, i.e., something
>> with a lot of end-user analysis code, instead of infrastructure.
>>
>> Wolfgang
>>>
>>>
>>>
>>>
>>>
>>>
>>> > On Dec 6, 2014, at 1:19 GMT+1, Michael Love <
>>> michaelisaiahlove at gmail.com> wrote:
>>> >
>>> > nice. I will play around with this. thanks Gabe!
>>> >
>>> > On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker <becker.gabe at gene.com>
>>> wrote:
>>> >> Hey guys,
>>> >>
>>> >> Surgically removed from promptClass:
>>> >>
>>> >> classInSig <- function(g, where, cl) {
>>> >> cl %in% unique(unlist(findMethods(g, where)@signatures))
>>> >> }
>>> >> genWithClass <- function(cl, where) {
>>> >> allgen <- getGenerics(where = where)
>>> >> ok <- as.logical(unlist(lapply(allgen, classInSig, cl = cl,
>>> >> where = where)))
>>> >> allgen[ok]
>>> >> }
>>> >>
>>> >>> genWithClass("IRanges", find(classMetaName("IRanges")))
>>> >> [1] "c" "coerce" "end<-" "gaps"
>>> "intersect"
>>> >> [6] "isNormal" "names<-" "names" "pgap"
>>> >> "pintersect"
>>> >> [11] "psetdiff" "punion" "reduce" "reverse"
>>> "setdiff"
>>> >> [16] "start<-" "start" "threebands" "union"
>>> >> "updateObject"
>>> >> [21] "update" "width<-" "width"
>>> >>
>>> >>
>>> >> For semantic guessing of which ones will be useful, I've got nothing
>>> (for
>>> >> now).
>>> >>
>>> >> ~G
>>> >>
>>> >> On Fri, Dec 5, 2014 at 11:28 AM, Michael Lawrence
>>> >> <lawrence.michael at gene.com> wrote:
>>> >>>
>>> >>> Cool. I see hypertext as being useful here, because the generics and
>>> >>> classes form an intricate and sometimes ambiguous web, especially when
>>> >>> multiple inheritance and dispatch are involved. I think we should
>>> first
>>> >>> build better tooling for introspecting S4 and for graph-based
>>> modeling and
>>> >>> analysis of S4 architecture. For example, could we statically detect
>>> >>> whether a dispatch ambiguity exists, knowing all of the methods and
>>> >>> classes? And based on that build one or more end-user UIs?
>>> >>>
>>> >>>
>>> >>>
>>> >>> On Fri, Dec 5, 2014 at 11:05 AM, Michael Love
>>> >>> <michaelisaiahlove at gmail.com>
>>> >>> wrote:
>>> >>>
>>> >>>> On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence
>>> >>>> <lawrence.michael at gene.com> wrote:
>>> >>>>>
>>> >>>>> I think this gets at the heart of at least one of the usability
>>> issues
>>> >>>> in Bioconductor: interface discoverability. Many simpler command line
>>> >>>> tools
>>> >>>> have a single-faceted interface for which it is easy to enumerate a
>>> list
>>> >>>> of
>>> >>>> features. There's definitely room for better ways to interrogate our
>>> >>>> object-oriented APIs, but it's challenging. Essentially we need a way
>>> >>>> for
>>> >>>> the user to ask "what can I do with this object?". Yes, we need
>>> better
>>> >>>> introspection utilities, but we also need to integrate the query with
>>> >>>> documentation. In other words, we need a more dynamic, more fluid
>>> help
>>> >>>> system, oriented around S4.
>>> >>>>>
>>> >>>>
>>> >>>> I would be interested in working on this. A minimal goal for me is a
>>> >>>> function that just returns a character vector of the names of the
>>> >>>> generics defined for the object. Filtering that down to give methods
>>> >>>> which are "likely relevant" using the documentation will definitely
>>> be
>>> >>>> a bigger challenge.
>>> >>>>
>>> >>>>
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> On Thu, Dec 4, 2014 at 9:56 AM, Michael Love <
>>> >>>> michaelisaiahlove at gmail.com> wrote:
>>> >>>>>>
>>> >>>>>> I was thinking about a request from someone at Bioc2014 (I can't
>>> >>>>>> remember at the moment)
>>> >>>>>>
>>> >>>>>> As an end-user, if I have an object x, how can I *quickly* recall
>>> the
>>> >>>>>> main methods for that? As in, without breaking my flow and going to
>>> >>>>>> ?myClass or help("myClass-class"). Suppose x is a GRanges, how can
>>> I
>>> >>>>>> remember that there is a method called narrow() which works on x?
>>> >>>>>>
>>> >>>>>> showMethods(classes=class(x)) will print out a huge list for many
>>> >>>>>> complex Bioc classes. And printTo=FALSE turns this huge list into
>>> an
>>> >>>>>> unhelpful character vector, e.g.:
>>> >>>>>>
>>> >>>>>> head(showMethods(classes="GRanges",printTo=FALSE),8)
>>> >>>>>> [1] "" "Function \".asSpace\":"
>>> >>>>>> [3] " <not an S4 generic function>" ""
>>> >>>>>> [5] "Function \".linkToCachedObject<-\":" " <not an S4 generic
>>> >>>> function>"
>>> >>>>>> [7] "" "Function
>>> >>>>>> \".replaceSEW\":"
>>> >>>>>>
>>> >>>>>> any ideas?
>>> >>>>>>
>>> >>>>>> _______________________________________________
>>> >>>>>> Bioc-devel at r-project.org mailing list
>>> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >>>>>
>>> >>>>>
>>> >>>>
>>> >>>
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>>> >>>
>>> >>> _______________________________________________
>>> >>> Bioc-devel at r-project.org mailing list
>>> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Computational Biologist
>>> >> Genentech Research
>>> >
>>> > _______________________________________________
>>> > Bioc-devel at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
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>>>
>>
>>
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