From murdoch at stats.uwo.ca  Tue Apr 22 15:24:24 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 22 Apr 2008 09:24:24 -0400
Subject: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in
 2.7.0	RC
In-Reply-To: <1A68FCB28DE72F4BA3B967E6506CCE4302294881@mildnpexmb01.maninvestments.ad.man.com>
References: <1A68FCB28DE72F4BA3B967E6506CCE430229487F@mildnpexmb01.maninvestments.ad.man.com>
	<480DD38A.7090004@stats.uwo.ca>
	<1A68FCB28DE72F4BA3B967E6506CCE4302294881@mildnpexmb01.maninvestments.ad.man.com>
Message-ID: <480DE708.3030104@stats.uwo.ca>

On 4/22/2008 9:08 AM, Sklyar, Oleg (MI London) wrote:
> 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:

I believe it is behaving as documented now, so the behaviour is 
"logical", even if it may not be convenient.  In your example

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

the 1st works in 2.6.2 and 2.7.0 and the second only works in 2.6.2. 
But the change below was designed to fix the case

plot(x)

which works in 2.7.0 and *not* in 2.6.2, so reverting the change is not 
the way to address this.

Duncan Murdoch

> 
> 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
Duncan Murdoch