[Bioc-devel] plotPCA for BiocGenerics

Kevin Coombes kevin.r.coombes at gmail.com
Mon Oct 20 20:30:22 CEST 2014

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
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 

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.coombes at gmail.com <mailto:kevin.r.coombes at 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"
>     <michaelisaiahlove at gmail.com <mailto:michaelisaiahlove at 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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