graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC

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

**********************************************************************

The contents of this email are for the named addressee(s) only.
It contains information which may be confidential and privileged.
If you are not the intended recipient, please notify the sender 
immediately, destroy this email and any attachments and do not 
otherwise disclose or use them. Email transmission is not a secure 
method of communication and Man Investments cannot accept 
responsibility for the completeness or accuracy of this 

email or any 

attachments. Whilst Man Investments makes every effort to keep its 
network free from viruses, it does not accept 

responsibility for any 

computer virus which might be transferred by way of this 

email or any 

attachments. This email does not constitute a request, offer, 
recommendation or solicitation of any kind to buy, 

subscribe, sell or 

redeem any investment instruments or to perform other such 
transactions of any kind. Man Investments reserves the right to 
monitor, record and retain all electronic communications 

through its 

network to ensure the integrity of its systems, for record 

keeping and 

regulatory purposes.

Visit us at: www.maninvestments.com