[Bioc-devel] recalling methods

[Michael Lawrence]

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

	[[alternative HTML version deleted]]