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

-----Original Message-----
From: Gabor Grothendieck [mailto:ggrothendieck at gmail.com] 
Sent: 22 April 2008 14:12
To: Sklyar, Oleg (MI London)
Cc: Duncan Murdoch; R-devel at r-project.org
Subject: Re: [Rd] graphics::Axis loosing S3/S4 class 
attributes of 'x' in 2.7.0 RC

This also affects Axis.yearmon and Axis.yearqtr in the zoo 
package which worked in R 2.6.2 and now don't work
properly.   It seems more logical to define plot.whatever
to handle the object in question, i.e. we do define plot.zoo, 
whereas only the Axis method ought to be required for the X 
and Y coordinate axes.

On Tue, Apr 22, 2008 at 8:53 AM, Sklyar, Oleg (MI London) 
<osklyar at maninvestments.com> wrote:

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;L

C_

MO

NETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_A

DD

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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