R help - Jul 2009 - Substituting a user-defined function for a standard function in graphics

Dear R-help readers,
     I'm trying to substitute my own version of plot.default, in order to
capture low-level graphics input for further manipulation.  I seem to be
having difficulties getting the versions of functions that I intend to use
called at the right places. 
     Specifically, I have an object produced by survfit from the survival
package, and I want to save the values that plot.survfit would normally
send to plot.default from the graphics package.  I've tried the following:

1. I put my version of plot.default into .GlobalEnv.  This works, in the
sense of running without an error, but doesn't do what I want, since my
version of plot.default never gets called, apparently because since the
version of plot comes from graphics, the graphics namespace takes
precedence over .GlobalEnv.

2. I put both my version of plot.default, and a copy of plot from graphics
(with a browser call on top, so that I know it's my version), into
.GlobalEnv. In this case, I get an error, apparently because my version of
plot hits the line UseMethod("plot"), can't see the survfit
method, and so
the fit gets dumped to plot.default, plot.default can only handle
arguments as defined in the graphics documentation on xy.coordinates, and
survfit isn't in this format.  I can't figure out why
UseMethod("plot")
doesn't send the survfit object to plot.survfit.  methods("plot")
gives
survfit with an asterisk (denoting invisibility); is the invisibility a
problem?

3. I made a package incorporating the graphics plot and my plot.default,
without a namespace file, and loaded it via a library call.  This again
gave me an error, since the survfit object seems to be sent directly to
plot.default rather than plot.survfit.

4. I made a package incorporating the graphics plot and my plot.default,
this time with a namesapce file that exports plot and plot.default. This
again gave me the same error, since the survfit object seems to be sent
directly to plot.default rather than plot.survfit.

I read the document Writing R Extensions, but wasn't able to solve this
problem.  Any pointers would be greatly appreciated.

Thanks, John Kolassa

On Jul 15, 2009, at 4:25 PM, John Kolassa wrote:
> Dear R-help readers,
>     I'm trying to substitute my own version of plot.default, in  
> order to
> capture low-level graphics input for further manipulation.  I seem  
> to be
> having difficulties getting the versions of functions that I intend  
> to use
> called at the right places.
>     Specifically, I have an object produced by survfit from the  
> survival
> package, and I want to save the values that plot.survfit would  
> normally
> send to plot.default from the graphics package.
So wouldn't you instead create a modified plot.survfit? Looking at the  
plot.survfit code, it appears that the only time plot is called is to  
set up the axes  (i.e. with ,type="n", )and then other functions are  
used to draw the curves.

<snipped recounting of unsuccessful efforts>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

On 15/07/2009 4:25 PM, John Kolassa wrote:
> Dear R-help readers,
>      I'm trying to substitute my own version of plot.default, in order
to
> capture low-level graphics input for further manipulation.  I seem to be
> having difficulties getting the versions of functions that I intend to use
> called at the right places. 
>      Specifically, I have an object produced by survfit from the survival
> package, and I want to save the values that plot.survfit would normally
> send to plot.default from the graphics package.  I've tried the
following:
That's probably hard, but it is very easy to get a copy of plot.survfit 
from the survival package source code, and modify it to your heart's 
content.

If you are doing something that would be useful to others, it might be a 
good idea to contact the maintainer of the survival package to ask him 
to incorporate your code, but you'd better have pretty high quality code 
before you ask for that.

Duncan Murdoch

> 1. I put my version of plot.default into .GlobalEnv.  This works, in the
> sense of running without an error, but doesn't do what I want, since my
> version of plot.default never gets called, apparently because since the
> version of plot comes from graphics, the graphics namespace takes
> precedence over .GlobalEnv.
> 
> 2. I put both my version of plot.default, and a copy of plot from graphics
> (with a browser call on top, so that I know it's my version), into
> .GlobalEnv. In this case, I get an error, apparently because my version of
> plot hits the line UseMethod("plot"), can't see the survfit
method, and so
> the fit gets dumped to plot.default, plot.default can only handle
> arguments as defined in the graphics documentation on xy.coordinates, and
> survfit isn't in this format.  I can't figure out why
UseMethod("plot")
> doesn't send the survfit object to plot.survfit. 
methods("plot") gives
> survfit with an asterisk (denoting invisibility); is the invisibility a
> problem?
> 
> 3. I made a package incorporating the graphics plot and my plot.default,
> without a namespace file, and loaded it via a library call.  This again
> gave me an error, since the survfit object seems to be sent directly to
> plot.default rather than plot.survfit.
> 
> 4. I made a package incorporating the graphics plot and my plot.default,
> this time with a namesapce file that exports plot and plot.default. This
> again gave me the same error, since the survfit object seems to be sent
> directly to plot.default rather than plot.survfit.
> 
> I read the document Writing R Extensions, but wasn't able to solve this
> problem.  Any pointers would be greatly appreciated.
> 
> Thanks, John Kolassa
> 
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