[Bioc-devel] recalling methods

[Wolfgang Huber]

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.

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)? 

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
>>>>> 
>>>>> 
>>>> 
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
>> 
>> --
>> Computational Biologist
>> Genentech Research
> 
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