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 <michaelisaiahl...@gmail.com> > wrote: > > nice. I will play around with this. thanks Gabe! > > On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker <becker.g...@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.mich...@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 >>> <michaelisaiahl...@gmail.com> >>> wrote: >>> >>>> On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence >>>> <lawrence.mich...@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 < >>>> michaelisaiahl...@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@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> >> -- >> Computational Biologist >> Genentech Research > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel