I understand that breaking code is a problem, and that is admittedly the
main reason not to immediately adopt my suggestion.
But as a purely logical exercise, creating a "PCA" object X or something
similar and using either
plot(X)
or
plot(as.PCA(mySpecialObject))
is a much more sensible use of object-oriented programming/design. This
requires no new generics (to write or to learn).
And you could use it to transition away from the current system by
convincing the various package maintainers to re-implement plotPCA as
follows:
plotPCA <- function(object, ...) {
plot(as.PCA(object), ...)
}
This would be relatively easy to eventually deprecate and teach users to
switch to the alternative.
On 10/20/2014 1:07 PM, Michael Love wrote:
> hi Kevin,
>
> that would imply there is only one way to plot an object of a given
> class. Additionally, it would break a lot of code.
>
> best,
>
> Mike
>
> On Mon, Oct 20, 2014 at 12:50 PM, Kevin Coombes
> <kevin.r.coom...@gmail.com <mailto:kevin.r.coom...@gmail.com>> wrote:
>
> But shouldn't they all really just be named "plot" for the
> appropriate objects? In which case, there would already be a
> perfectly good generic....
>
> On Oct 20, 2014 10:27 AM, "Michael Love"
> <michaelisaiahl...@gmail.com <mailto:michaelisaiahl...@gmail.com>>
> wrote:
>
> I noticed that 'plotPCA' functions are defined in EDASeq,
> DESeq2, DESeq,
> affycoretools, Rcade, facopy, CopyNumber450k, netresponse,
> MAIT (maybe
> more).
>
> Sounds like a case for BiocGenerics.
>
> best,
>
> Mike
>
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>
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