From murdoch at stats.uwo.ca  Tue May 26 21:30:10 2009
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 26 May 2009 15:30:10 -0400
Subject: [Rd] plot ignores type= "n" when x is factor (PR#13703)
In-Reply-To: <d8ad40b50905261038i2a8e9ad7v93ec798320e19d87@mail.gmail.com>
References: <20090514193515.9BC3528320DF@mail.pubhealth.ku.dk>	<alpine.LFD.2.00.0905260852140.22101@gannet.stats.ox.ac.uk>	<13e802630905260958j3ab9e060rec4695697f024c6a@mail.gmail.com>
	<d8ad40b50905261038i2a8e9ad7v93ec798320e19d87@mail.gmail.com>
Message-ID: <4A1C4342.1000107@stats.uwo.ca>

On 5/26/2009 1:38 PM, Barry Rowlingson wrote:
> On Tue, May 26, 2009 at 5:58 PM, Paul Johnson <pauljohn32 at gmail.com> wrote:
> 
>> There's no mention of plot.factor in the plot help page.
> 
> Yes there is, but hidden slightly more than the planning application
> for the destruction of the Earth ("It was on display in the bottom of
> a locked filing cabinet stuck in a disused lavatory with a sign on the
> door saying 'Beware of the Leopard'"[1]). Here it is:
> 
> See Also:
> 
>      'plot.default', 'plot.formula' and other methods; 'points',
>      'lines', 'par'.
> 
>  see that 'other methods'? That's it. That's a clue. That's our
> 'beware of the leopard'. So you need to know about methods...
> 
>> How about inserting this at the top of the help page for plot:
>>
>> If either x or y is a factor variable, the plot.factor method is
>> called to determine the sort of graph to be drawn. If x and y are both
>> numeric, the type argument determines the sort of graph to be drawn.
> 
>  Ah, but something like that would need inserting at the top of just
> about every function. R has 'generic' functions that call specific
> functions for specific types of object. In two (or more) different
> ways. I'm not sure if there's an easy way to say 'get me the help for
> the specific method for this thing X when I do foo(X)'.

There is, though it only works if X has an S4 class, so it doesn't work 
in this particular case.  You just use

?foo(X)

The mechanism could be extended to S3 classes by guessing that functions 
always dispatch on the class of the first argument, and that might be 
better than what we have now, but there's a lot of guesswork involved.

Duncan Murdoch

> 
>  You can try: methods(class=class(factor(c(1,2,3,1)))) which will show
> 'plot.factor' as one of the possible things you can do with factor
> objects. Then you can do help(plot.factor). You can also do
> methods(plot) to show all the different classes that the generic plot
> function can work on. But note these are 'S3' methods - once you hit
> "S4" methods you'll need something else.
> 
>  And you can hit S4 methods in cruel and unusual ways. For example:
> 
>  > library(sp)
>  > plot
>  standardGeneric for "plot" defined from package "graphics"
> 
> function (x, y, ...)
> standardGeneric("plot")
> <environment: 0x842c6d8>
> Methods may be defined for arguments: x, y
> Use  showMethods("plot")  for currently available ones.
> 
>  Ooh, let's try that:
> 
>  > showMethods("plot")
>  Function: plot (package graphics)
>  x="ANY", y="ANY"
>  x="SpatialLines", y="missing"
>  x="Spatial", y="missing"
>  x="SpatialPoints", y="missing"
>  x="SpatialPolygons", y="missing"
> 
>  - no mention of factor there. That's because the sp package has
> fiddled with the generic plot function to make it S4-compatible. The
> S3 methods still work, but now you get added S4 method goodness.
> 
>  Yes, the plot function has changed in the middle of your R session.
> And this isn't "mostly harmless[1]". Some code I wrote broke because
> the new definition of 'plot' was evaluating the 'y' when I didn't want
> it to. The previous definition didn't evaluate y until it got to my
> generic function.
> 
>> If you did that, then you could answer my bug report with the
>> criticism that I did not read ?plot.factor or that plot.factor can't
>> do what I want. Otherwise, your response seems unkind and somewhat
>> unreasonable.  I have no way of knowing that plot.factor is even
>> involved when I try to use the plot function.
> 
>  Perhaps an unkind and unreasonable response serves to shock people
> into remembering these things -  people on the end of such treatment
> don't seem to return to ask very many more questions...
> 
> Barry
> 
> [1] Hitchhikers' Guide To The Galaxy, Douglas Adams
> 
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> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] plot ignores type= "n" when x is factor (PR#13703)
Duncan Murdoch