From christos.hatzis at nuverabio.com  Sun Mar 16 05:40:25 2008
From: christos.hatzis at nuverabio.com (Christos Hatzis)
Date: Sun, 16 Mar 2008 00:40:25 -0400
Subject: [Rd] [patch] add=TRUE in plot.default()
In-Reply-To: <20080316040518.GG21820@econ.upenn.edu>
References: <20080309031119.GC23544@econ.upenn.edu><47D40C41.1000202@stats.uwo.ca><20080309164639.GF23544@econ.upenn.edu><47D442B8.10501@stats.uwo.ca><20080309215833.GH23544@econ.upenn.edu><47D52ECB.8000709@stats.uwo.ca>
	<20080316040518.GG21820@econ.upenn.edu>
Message-ID: <002301c8871f$daa08cf0$0202a8c0@headquarters.silicoinsights>

Andrew,

Here's is a way how your example could be coded with the current
implementation of plot.  You can always start with an empty plot and then
add lines or points (or both) using the corresponding functions.  

> x <- seq(-2, 2, 0.1)
> plot(x, x, type="n")
> mapply(function(f, i) lines(x, f(x), col=i), functions, 1:3)

The current approach saves specification of a couple of parameters that
would otherwise had to be specified, since lines(...) would be equivalent to
plot(..., type="l", add=TRUE), and I think that this adds to clarity.

-Christos
 
> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Andrew Clausen
> Sent: Sunday, March 16, 2008 12:05 AM
> To: Duncan Murdoch
> Cc: R-devel at r-project.org
> Subject: Re: [Rd] [patch] add=TRUE in plot.default()
> 
> Hi Duncan,
> 
> On Mon, Mar 10, 2008 at 08:51:23AM -0400, Duncan Murdoch wrote:
> > >The add parameter only interacts with other parameters 
> superficially 
> > >-- some parameters of "plot" (like log) are related to the 
> shape of 
> > >the axes, and should be inherited from what is on the plot already.
> > 
> > I'd say causing some parameters to be completely ignored without a 
> > warning is more than a superficial interaction.
> 
> Fair enough.  I suppose you could inadvertantly put leave 
> "add=TRUE" in some code, and wonder why axes aren't getting drawn.
> 
> > Really, add=TRUE is not
> > a great design:  it would be better to say "plot methods draw a new 
> > plot" (so they need args for all the decorations like axes, titles, 
> > etc.), and have other ways to add things to plots.
> 
> I don't like the idea of having a separate way to add to plots.
> I like the look of this code:
> 
> 	f <- function(x) x^2
> 	g <- function(x) 1/x - 1
> 	h <- function(x) x
> 	functions <- c(f, g, h)
> 	for (i in 1:length(functions))
> 		plot(functions[[i]], add=i>1, col=i)
> 
> Of course, I'd prefer something like
> 
> 	plot.new()
> 	for (i in 1:length(functions))
> 		plot(functions[[i]], add=TRUE, col=i)
> 
> but that seems out of reach for compatibility reasons.
> 
> How would you write this code in R today?
> 
> >  Hadley was right on
> > this, his ggplot2 has a better thought-out design than 
> classic graphics. 
> >   However, we have what we have.
> 
> I'm sure ggplot2 is vastly better, although I couldn't find a 
> quick intro.
> (Typing "ggplot2 examples" into Google didn't help me.)  
> Since plot() isn't deprecated yet, it's worth making cheap 
> useful improvements.
> 
> > >I agree.  Adding an "add=FALSE" parameter to plot() would generate 
> > >errors for methods that don't implement it, so they would 
> all have to 
> > >be changed simultaneously, including in private/unreleased code.
> > >
> > >So I'd like to settle for second best: adding add=FALSE 
> parameters to 
> > >many plot methods.
> > 
> > I like that suggestion better than adding it here and 
> there, one at a 
> > time.  So, to advance the discussion:  can you take a look 
> at the plot 
> > methods that are in the base and recommended packages, and work out 
> > how many already have it, how many would be improved if it 
> was added, 
> > and in how many cases it just wouldn't make sense?  (You 
> could also do 
> > this on all the CRAN and Bioconductor packages, but that would be 
> > about 100 times more work: about 50 times as many packages, 
> and much 
> > less consistency in the programming and documentation standards.  
> > Maybe on a subset of popular ones, e.g. those that Rcmdr suggests?)
> 
> I had a quick look at the base packages.  (I did a crude 
> search with find and grep on the R source tarball.)  I 
> attached the full list.  There were 40 files
> containing plot methods.   Of these, 9 already implemented 
> add=TRUE explicitly
> and a further 9 inherited it from other plot methods that 
> could or already do implement it.  There were 2 methods for 
> which it clearly makes no sense.  For example, plot.lm makes 
> no sense because it does several separate plots, one after the other.
> 
> It looks reasonably straightforward to implement most of the 
> remaining methods.
> I must confess I don't understand what all of these plots are 
> doing from a statistics point of view, but I suppose this 
> shouldn't matter.  (Econometrics uses different language...)
> 
> > Data like that could make a convincing argument that the effort of 
> > adding this to the base packages is worthwhile.  (To get it 
> added to 
> > non-base packages will require you to convince their 
> maintainers that 
> > it's a good idea.)  Another helpful part of the argument 
> will be for 
> > you to volunteer to do the work of both code and 
> documentation updates.
> 
> I'm not very excited about doing work outside of base.  I can 
> do the base code + documentation though.  Any volunteers?
> 
> Cheers,
> Andrew
> 
>



[Rd] [patch] add=TRUE in plot.default()
Christos Hatzis