Just to bring the discussion back to the fact that there is a need to do
/something/. A function plotPCA is defined in packages EDASeq, DESeq2, DESeq,
affycoretools, Rcade, facopy, CopyNumber450k, netresponse, MAIT, with a real
potential for needless user confusion. And BiocGenerics already
whatever, here's a patch. If BiocGenerics had a GitHub repo I'd just
submit a pull request. Bounce it or don't, it took 5 minutes of a Sunday
morning for a non-core committer, so it must not be that hard to build a
bikeshed after all. /s
FWIW I once remarked to Robert Gentleman that it seemed
On Sun, Nov 2, 2014 at 12:19 AM, Wolfgang Huber whu...@embl.de wrote:
Just to bring the discussion back to the fact that there is a need to do
/something/. A function plotPCA is defined in packages EDASeq, DESeq2,
DESeq, affycoretools, Rcade, facopy, CopyNumber450k, netresponse, MAIT,
with a
I guess I'm thinking now to move toward breaking up the PCA and plot
in DESeq2, given that there is non-trivial computation going on, and
then to leave plotPCA as a wrapper and to avoid breaking any user
code. We had already moved this way a bit, in that in the current
release, plotPCA has an
I see the argument for separating plotting and computation.
I don't see the argument for changing plotPCA to plot. base R has things
that work either way; we all know hist(), boxplot() etc etc. And for this
specific case there are (good) arguments for the fact that one could
envision several
With regards to abstraction - I would personally much rather read and write
code that contained plotScores() and plotScree() etc. where the intend of the
code is clearly communicated, instead of relying on a plot() function whose
result is only known from experience. Trying to squeeze every
Hi,
On Fri, Oct 31, 2014 at 2:35 PM, Thomas Lin Pedersen
thomas...@gmail.com wrote:
With regards to abstraction - I would personally much rather read and write
code that contained plotScores() and plotScree() etc. where the intend of the
code is clearly communicated, instead of relying on a
While I tend to agree with you that PCA is too big an operation to be hidden
within a plotting function (MDS is an edge-case I would say), I can’t see how
we can ever reach a point where there is only one generic plot function. In the
case of PCA there is a number of different plot-types that
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
wrote:
But shouldn't they all really just be named plot for the appropriate
I agree it depends on programming style. But to continue with the example,
it would have to be:
plot(as.mySpecialObjectPCA(mySpecialObject))
because we have many packages here with their own functions.
Wouldn't this just proliferate the number of classes instead of functions?
For every type of
Hi,
It depends.
The traditional R approach to these matters is that you (a) first
perform some sort of an analysis and save the results as an object and
then (b) show or plot what you got. It is part (b) that tends to be
really generic, and (in my opinion) should have really generic names --
Hi,
I don't see how it needs more functions (as long as you can get
developers to agree). Suppose that someone can define a reusable PCA
class. This will contain a single plot generic function, defined once
and reused by other classes. The existing plotPCA interface can also
be implemented
Ah, I see now. Personally, I don't think Bioconductor developers should
have to agree on single plotting functions for basic classes like 'PCA'
(because this logic applies equally to the situation of all Bioconductor
developers agreeing on single MA-plot, a single variance-mean plot, etc). I
think
Well. I have two responses to that.
First, I think it would be a lot better/easier for users if (most)
developers could make use of the same plot function for basic classes
like PCA.
Second, if you think the basic PCA plotting routine needs enhancements,
you still have two options. On the
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