From osklyar at maninvestments.com  Tue Apr 22 15:08:56 2008
From: osklyar at maninvestments.com (Sklyar, Oleg (MI London))
Date: Tue, 22 Apr 2008 14:08:56 +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: <1A68FCB28DE72F4BA3B967E6506CCE4302294881@mildnpexmb01.maninvestments.ad.man.com>

Duncan,

looking further, what has changed from 2.6.2 into 2.7.0 are the
following two lines in plot.default, which I think were logical before
and are not really logical now:

plot.R: plot.default (2.6.2):
if (axes) {
	localAxis(x, side=1, ...)
	localAxis(y, side=2, ...)
}

plot.R: plot.default (2.7.0):
...
if (axes) {
	localAxis(xy$x, side=1, ...)
	localAxis(xy$y, side=2, ...)
}

The fact that xy.coords is called does not really matter.


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