From osklyar at maninvestments.com  Tue Apr 22 14:53:39 2008
From: osklyar at maninvestments.com (Sklyar, Oleg (MI London))
Date: Tue, 22 Apr 2008 13:53:39 +0100
Subject: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in
	2.7.0	RC
In-Reply-To: <480DD38A.7090004@stats.uwo.ca>
References: <1A68FCB28DE72F4BA3B967E6506CCE430229487F@mildnpexmb01.maninvestments.ad.man.com>
	<480DD38A.7090004@stats.uwo.ca>
Message-ID: <1A68FCB28DE72F4BA3B967E6506CCE4302294880@mildnpexmb01.maninvestments.ad.man.com>

Thanks Duncan,

this might explain why Axis.MyClass is never called.

However, it is really not only illogical to define plot.MyClass instead
of Axis.MyClass if the only thing I want is formatting of the axis, but
it is also broken in R 2.7.0 and here is why.

Let's forget about MyClass and take POSIXct, for which plot.POSIXct and
Axis.POSIXct are defined in graphics. First question would be, why
define Axis.POSIXct if it is logical to just define plot.POSIXct. But
then, try the following example in 2.7.0 and 2.6.2:

x = Sys.time() + runif(100,1,7200) ## time over two hours, POSIXct
plot(x,1:100)
plot(1:100,x)

The first plot will be correctly formatted in both R versions while the
second one will be *incorrectly* formatted in 2.7.0 (funny enough
xy.coords returns as.double in both, so that might not be the reason for
the problem).

What happens is that plot.POSIXct is called in the former case and thus
we get the correct formatting. However, plot.default is called in the
latter case. In 2.6.2 Axis.POSIXct was the reason why y axis was
correctly formatted here. In 2.7.0 Axis.default is called instead
because class of x is reset.

Now this perfectly indicates why it is logical to have Axis.MyClass
defined (as this two-liner would be called in all possible situations
producing correct axes independently where it is called from) and not
plot.MyClass (which would actually not cover the situation of only the
second argument being MyClass). Surely I can define S4 with multiple
signatures, but logically I would define Axis.MyClass.

Omitting axes completely is not a good options to enforce on users for
default plots, is it?


Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
osklyar at maninvestments.com 

> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca] 
> Sent: 22 April 2008 13:01
> To: Sklyar, Oleg (MI London)
> Cc: R-devel at r-project.org
> Subject: Re: [Rd] graphics::Axis loosing S3/S4 class 
> attributes of 'x' in 2.7.0 RC
> 
> On 22/04/2008 7:25 AM, Sklyar, Oleg (MI London) wrote:
> > Following my previous post on S3 method despatch, I put 
> debug messages 
> > in the code of Axis, Axis.default and plot.default in 
> > graphics/R/axis.R and graphics/R/plot.R to print the class of x, at 
> > and y on plot. After recompiling R, what I see is that x *lost* its 
> > class attribute (at least for classes not known to 'graphics') in 
> > Axis, called directly from plot.default and this could be 
> the reason 
> > why R did not despatch on Axis.MyClass from my previous post. This 
> > happens for both S3 and S4 classes as in the code below! 
> Funny enough, 
> > even "integer" was reset to numeric in Axis...
> 
> If you look at plot.default, you'll see it passes x and y 
> through xy.coords to get coordinates.  That function ends with
> 
> return(list(x=as.double(x), y=as.double(y), xlab=xlab, ylab=ylab))
> 
> so that's where classes get removed.  If you don't want this 
> to happen, shouldn't you be defining plot.MyClass, or calling 
> the default with axes=F, and then calling Axis on your object 
> yourself?
> 
> > Is this really an intended behaviour? It looks very wrong to me!
> 
> This is documented:  ?plot.default tells you to look at 
> ?xy.coords for details of how x and y are handled, and 
> xy.coords says "In any other case, the 'x' argument is 
> coerced to a vector and
>       returned as *y* component where the resulting 'x' is just the
>       index vector '1:n'.  In this case, the resulting 'xlab' 
> component
>       is set to '"Index"'."
> 
> Duncan Murdoch
> 
> > Thanks,
> > Oleg
> > 
> > *** R version 2.7.0 RC (2008-04-20 r45403) 
> [/research/osklyar/R-devel]
> > ***
> >> Axis
> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
> >     cat("In Axis() class(x)=", class(x), "; class(at)=", class(at),
> >         "\n", sep = "")
> >     if (!is.null(x))
> >         UseMethod("Axis", x)
> >     else if (!is.null(at))
> >         UseMethod("Axis", at)
> >     else axis(side = side, at = at, labels = labels, ...) }
> > <environment: namespace:graphics>
> >> graphics:::Axis.default
> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
> >     cat("In Axis.default() class(x)=", class(x), "; class(at)=",
> >         class(at), "\n", sep = "")
> >     if (is.null(at) && !is.null(x))
> >         at = pretty(x)
> >     axis(side = side, at = at, labels = labels, ...) }
> > <environment: namespace:graphics>
> >> setClass("MyClass", representation(smth="character"),
> > contains="numeric")
> > [1] "MyClass"
> >> a = new("MyClass", runif(10))
> >> a
> > An object of class "MyClass"
> >  [1] 0.773237167 0.548630205 0.987956687 0.212667925 0.337135151
> > 0.112210501
> >  [7] 0.007140895 0.972028903 0.443581963 0.536452424 Slot "smth":
> > character(0)
> >> plot(1:10,a)
> > In plot.default() class(x)=integer; class(y)=MyClass In Axis() 
> > class(x)=numeric; class(at)=NULL In Axis.default() 
> class(x)=numeric; 
> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In 
> > Axis.default() class(x)=numeric; class(at)=NULL
> >> plot(a,1:10)
> > In plot.default() class(x)=MyClass; class(y)=integer In Axis() 
> > class(x)=numeric; class(at)=NULL In Axis.default() 
> class(x)=numeric; 
> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In 
> > Axis.default() class(x)=numeric; class(at)=NULL
> >> b = runif(10)
> >> class(b)="AnotherClass"
> >> plot(b,1:10)
> > In plot.default() class(x)=AnotherClass; class(y)=integer In Axis() 
> > class(x)=numeric; class(at)=NULL In Axis.default() 
> class(x)=numeric; 
> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In 
> > Axis.default() class(x)=numeric; class(at)=NULL
> >> plot(1:10)
> > In plot.default() class(x)=integer; class(y)=NULL In Axis() 
> > class(x)=numeric; class(at)=NULL In Axis.default() 
> class(x)=numeric; 
> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In 
> > Axis.default() class(x)=numeric; class(at)=NULL>
> >> sessionInfo()
> > R version 2.7.0 RC (2008-04-20 r45403) x86_64-unknown-linux-gnu
> > 
> > locale:
> > 
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=C;LC_
> > MO 
> > 
> NETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADD
> > RE 
> SS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> > 
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> > 
> > 
> > Dr Oleg Sklyar
> > Technology Group
> > Man Investments Ltd
> > +44 (0)20 7144 3803
> > osklyar at maninvestments.com
> > 
> > 
> > 
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[Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Sklyar, Oleg (MI London