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

Tue, Apr 22, 2008 7:26 AM

Ok, so what's wrong with the following fix for plot(x) that would
actually fix what needs to be fixed instead of changing plot.default?
Fix means reverting plot.default in 2.7.0 to what it was (if testing in
2.7.0, copy and paste the OLD plot.default into the .GlobalEnv):

plot.POSIXct <- function(x, y, xlab = "", ...) {
    if (!missing(y)) {
        side = 1
        plotDef <- function(x, y, xaxt, xlab, ...) plot.default(x, y,
xaxt="n", xlab=xlab, ...)
        plotDef(x, y, xlab=xlab, ...)
    } else {
        side = 2
        plotDef <- function(x, y, yaxt, xlab, ...) plot.default(x, y,
yaxt="n", xlab=xlab, ...)
        plotDef(seq_along(x), x, xlab=xlab, ...)
    }
    ## trick to remove arguments intended for title() or plot.default()
    axisInt <- function(x, type, main, sub, xlab, ylab, col, lty, lwd,
                        xlim, ylim, bg, pch, log, asp, axes, frame.plot,
...)
        axis.POSIXct(side, x, ...)
    dots <- list(...)
    axes <- if("axes" %in% names(dots)) dots$axes else TRUE
    xaxt <- if("xaxt" %in% names(dots)) dots$xaxt else par("xaxt")
    if(axes && xaxt != "n") axisInt(x, ...)
}

plot.POSIXlt <- function(x, y, xlab = "", ...) {
    if (missing(y)) plot.POSIXct(as.POSIXct(x), xlab=xlab, ...)
    else plot.POSIXct(as.POSIXct(x), y=y, xlab=xlab, ...)
}

And try with:
x = Sys.time() + runif(100,1,7200)
plot(x)
plot(x,1:100)
plot(1:100,x)

plot(as.POSIXlt(x))
plot(as.POSIXlt(x),1:100)
plot(1:100,as.POSIXlt(x))


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 14:24
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 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_AD

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

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