R devel - Mar 2016 - Different results based on the order of arguments to par

I ran into this issue when trying to modify a subplot (subplot
function in the TeachingDemos package), but here is a more minimal
example of the issue (I don't know that it is serious enough to call a
bug):

This code works how I expect:

dev.new()
hist(rexp(100))

par(plt=c(0.5,0.9,0.5,0.77), usr=c(0,1,0,1))

box() # show new plt region
points(c(0,1), c(0,1), pch=16, col='red', cex=3)

it creates a histogram then changes the plotting region so that I can
add an annotation, changes the user coordinates within the new region,
then plots some points using the new coordinate system.

But if I change the order of the arguments to par like so:

dev.new()
hist(rexp(100))

par(usr=c(0,1,0,1), plt=c(0.5,0.9,0.5,0.77))

box() #show new plt region
points(c(0,1), c(0,1), pch=16, col='red')

then the points do not show up (or if we add xpd=NA to the par call
then we see them outside of the plotting region).  So clearly the
behavior of par depends on the order of the arguments specified.

This is not explicitly documented, though there is a hinting at the
behavior in the note on the par help page (it was following this
warning that led to me first encountering the issue, since I was
specifying only the parameters that I needed, not everything, and
happened to specify usr before plt), but "usr" is not included in the
list in the note (because it does something different from what the
note is specifically warning about).


I see a few different potential responses to this issue:

1. consider that this is a rare enough issue that only Greg Snow will
ever care and he has already learned the lesson, so do nothing (other
than laugh at Greg when he forgets and has to remember to properly
order his par arguments).

2. Since this came up as an issue with subplot, force the author of
subplot and the TeachingDemos package to add a note or warning to the
documentation for that function.

3.  Expand the note on the help page for par (or add another note)
that warns that the order of the parameters matters and to therefore
be careful in which order you specify arguments (probably with some
detail on the suggested ordering).  While there will be many users who
never read this, we will at least be able to point to the note if
anyone else is affected by this issue.

4. Modify the par function to reorder the list created from its args
so that they are evaluated in a consistent order (and probably add
documentation to the help page to this effect).


Thoughts?




-- 
Gregory (Greg) L. Snow Ph.D.
538280 at gmail.com

Hi

I'm going to try to blame user error here.

par(usr) is used to reset the coordinates on the CURRENT plot.

par(plt) is used to specify the location of the NEXT plot.

The correct approach should be to set up the location for the next plot, 
start a new plot, set up coordinates on the new plot.

Neither of your examples performs the "start a new plot" step.

I would expect to see something like ...

dev.new()
hist(rexp(100))
# Set up location of new plot
par(plt=c(0.5,0.9,0.5,0.77))
# Avoid new page
par(new=TRUE)
# Start new plot
plot.new()
# Set up coordinates on new plot
# (though plot.window() might be better here)
par(usr=c(0,1,0,1))
# Start drawing
box()
points(c(0,1), c(0,1), pch=16, col='red', cex=3)

Is there a good argument against doing that?

Paul

On 15/03/16 10:27, Greg Snow wrote:
> I ran into this issue when trying to modify a subplot (subplot
> function in the TeachingDemos package), but here is a more minimal
> example of the issue (I don't know that it is serious enough to call a
> bug):
>
> This code works how I expect:
>
> dev.new()
> hist(rexp(100))
>
> par(plt=c(0.5,0.9,0.5,0.77), usr=c(0,1,0,1))
>
> box() # show new plt region
> points(c(0,1), c(0,1), pch=16, col='red', cex=3)
>
> it creates a histogram then changes the plotting region so that I can
> add an annotation, changes the user coordinates within the new region,
> then plots some points using the new coordinate system.
>
> But if I change the order of the arguments to par like so:
>
> dev.new()
> hist(rexp(100))
>
> par(usr=c(0,1,0,1), plt=c(0.5,0.9,0.5,0.77))
>
> box() #show new plt region
> points(c(0,1), c(0,1), pch=16, col='red')
>
> then the points do not show up (or if we add xpd=NA to the par call
> then we see them outside of the plotting region).  So clearly the
> behavior of par depends on the order of the arguments specified.
>
> This is not explicitly documented, though there is a hinting at the
> behavior in the note on the par help page (it was following this
> warning that led to me first encountering the issue, since I was
> specifying only the parameters that I needed, not everything, and
> happened to specify usr before plt), but "usr" is not included in
the
> list in the note (because it does something different from what the
> note is specifically warning about).
>
>
> I see a few different potential responses to this issue:
>
> 1. consider that this is a rare enough issue that only Greg Snow will
> ever care and he has already learned the lesson, so do nothing (other
> than laugh at Greg when he forgets and has to remember to properly
> order his par arguments).
>
> 2. Since this came up as an issue with subplot, force the author of
> subplot and the TeachingDemos package to add a note or warning to the
> documentation for that function.
>
> 3.  Expand the note on the help page for par (or add another note)
> that warns that the order of the parameters matters and to therefore
> be careful in which order you specify arguments (probably with some
> detail on the suggested ordering).  While there will be many users who
> never read this, we will at least be able to point to the note if
> anyone else is affected by this issue.
>
> 4. Modify the par function to reorder the list created from its args
> so that they are evaluated in a consistent order (and probably add
> documentation to the help page to this effect).
>
>
> Thoughts?
>
>
>
>
-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/

Paul,

I was trying to make a minimal self contained example, but I guess I
went too far on the minimizing.  The original problem came from code
more like:

library(TeachingDemos)

hist(rexp(1000), main='')
abline( v=1, col='red')

sp.par <- subplot(hist(rnorm(100), main=''), x='topright')

op <- par(sp.par[c('usr', 'plt')])
abline(v=0, col='red')
par(op)

and so plot.new, plot.window, etc. are called as part of the sub plot
(specifically by hist(rnorm(100))) and I am trying to go back and add
a reference line to the subplot so the user coordinates need to be set
back to match the subplot (and the plotting region needs to be set so
that the line is clipped appropriately).  With the code as above the
user coordinates are not changed appropriately, in fact if 'xpd=NA' is
added to the par call then the vertical line is added at 0 on the big
histogram, not the little one as planned.

If the order is changed in the call to par ( op <-
par(sp.par[c('plt','usr')]) ) then everything works as planned. 
It
just seems a potential danger to have different behavior when the
order of the arguments change without this fact at least documented.

Maybe a warning and additional examples in the subplot documentation
will be sufficient, since nobody else seems to have complained about
this yet.  But, I am vain enough to think that somewhere in the world
there is someone else who will make as stupid a mistake as me, so
wanted to make others aware.  If nothing else, the next person (which
may be forgetful future me) may see this in a search and at least know
to order the arguments correctly.


On Mon, Mar 14, 2016 at 7:04 PM, Paul Murrell <paul at
stat.auckland.ac.nz> wrote:
> Hi
>
> I'm going to try to blame user error here.
>
> par(usr) is used to reset the coordinates on the CURRENT plot.
>
> par(plt) is used to specify the location of the NEXT plot.
>
> The correct approach should be to set up the location for the next plot,
> start a new plot, set up coordinates on the new plot.
>
> Neither of your examples performs the "start a new plot" step.
>
> I would expect to see something like ...
>
> dev.new()
> hist(rexp(100))
> # Set up location of new plot
> par(plt=c(0.5,0.9,0.5,0.77))
> # Avoid new page
> par(new=TRUE)
> # Start new plot
> plot.new()
> # Set up coordinates on new plot
> # (though plot.window() might be better here)
> par(usr=c(0,1,0,1))
> # Start drawing
> box()
> points(c(0,1), c(0,1), pch=16, col='red', cex=3)
>
> Is there a good argument against doing that?
>
> Paul
>
>
> On 15/03/16 10:27, Greg Snow wrote:
>>
>> I ran into this issue when trying to modify a subplot (subplot
>> function in the TeachingDemos package), but here is a more minimal
>> example of the issue (I don't know that it is serious enough to
call a
>> bug):
>>
>> This code works how I expect:
>>
>> dev.new()
>> hist(rexp(100))
>>
>> par(plt=c(0.5,0.9,0.5,0.77), usr=c(0,1,0,1))
>>
>> box() # show new plt region
>> points(c(0,1), c(0,1), pch=16, col='red', cex=3)
>>
>> it creates a histogram then changes the plotting region so that I can
>> add an annotation, changes the user coordinates within the new region,
>> then plots some points using the new coordinate system.
>>
>> But if I change the order of the arguments to par like so:
>>
>> dev.new()
>> hist(rexp(100))
>>
>> par(usr=c(0,1,0,1), plt=c(0.5,0.9,0.5,0.77))
>>
>> box() #show new plt region
>> points(c(0,1), c(0,1), pch=16, col='red')
>>
>> then the points do not show up (or if we add xpd=NA to the par call
>> then we see them outside of the plotting region).  So clearly the
>> behavior of par depends on the order of the arguments specified.
>>
>> This is not explicitly documented, though there is a hinting at the
>> behavior in the note on the par help page (it was following this
>> warning that led to me first encountering the issue, since I was
>> specifying only the parameters that I needed, not everything, and
>> happened to specify usr before plt), but "usr" is not
included in the
>> list in the note (because it does something different from what the
>> note is specifically warning about).
>>
>>
>> I see a few different potential responses to this issue:
>>
>> 1. consider that this is a rare enough issue that only Greg Snow will
>> ever care and he has already learned the lesson, so do nothing (other
>> than laugh at Greg when he forgets and has to remember to properly
>> order his par arguments).
>>
>> 2. Since this came up as an issue with subplot, force the author of
>> subplot and the TeachingDemos package to add a note or warning to the
>> documentation for that function.
>>
>> 3.  Expand the note on the help page for par (or add another note)
>> that warns that the order of the parameters matters and to therefore
>> be careful in which order you specify arguments (probably with some
>> detail on the suggested ordering).  While there will be many users who
>> never read this, we will at least be able to point to the note if
>> anyone else is affected by this issue.
>>
>> 4. Modify the par function to reorder the list created from its args
>> so that they are evaluated in a consistent order (and probably add
>> documentation to the help page to this effect).
>>
>>
>> Thoughts?
>>
>>
>>
>>
>
> --
> Dr Paul Murrell
> Department of Statistics
> The University of Auckland
> Private Bag 92019
> Auckland
> New Zealand
> 64 9 3737599 x85392
> paul at stat.auckland.ac.nz
> http://www.stat.auckland.ac.nz/~paul/


-- 
Gregory (Greg) L. Snow Ph.D.
538280 at gmail.com