R help - Apr 2008 - plotmath "overstrikes" in output on a Linux system

I've been testing plotmath.  But I'm getting some funny output one one
computer. The problem is that characters are 'jumbled' and overstrike
when symbols are introduced.

Sample code:

mu <- 440.0
sigma <- 12.5
myx <- seq( mu - 4*sigma,  mu+ 4*sigma, length.out=500)
myDensity <- dnorm(myx,mean=mu,sd=sigma)

# Here's one way to retrieve the values of mu and sigma and insert
them into an expression
t1t2 <- bquote (paste("Normal(", mu== .(mu), ',', sigma==
.(sigma),")") )

plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)


I have tested this code and it works on two desktop Fedora Linux 8
systems to make a nice figure, but on a Dell Laptop with Fedora Linux
8 and R 2.6.2, something funny happens: the characters "overstrike"
each other.  The Greek letter "mu" is printed several spaces to the
left of the "(" that it is supposed to follow.  I made an itty  bitty
picture of the figure title to show you:

http://pj.freefaculty.org/R/plotmath_problem.png

I can force in spaces to re-arrange the symbols so they do not
overstrike. The following looks fine in the output.


t1t2 <- bquote (paste("Normal (   ", mu== .(mu), '  ,  ',
sigma=.(sigma)," )") )
### Note spaces manually inserted above are needed, otherwise plotmath
overlaps "l" of

plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)


What do you suppose is wrong? The X configuration?


-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

Paul Johnson wrote:
> I've been testing plotmath.  But I'm getting some funny output one
one
> computer. The problem is that characters are 'jumbled' and
overstrike
> when symbols are introduced.
>
> Sample code:
>
> mu <- 440.0
> sigma <- 12.5
> myx <- seq( mu - 4*sigma,  mu+ 4*sigma, length.out=500)
> myDensity <- dnorm(myx,mean=mu,sd=sigma)
>
> # Here's one way to retrieve the values of mu and sigma and insert
> them into an expression
> t1t2 <- bquote (paste("Normal(", mu== .(mu), ',',
sigma== .(sigma),")") )
>
> plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)
>
>
> I have tested this code and it works on two desktop Fedora Linux 8
> systems to make a nice figure, but on a Dell Laptop with Fedora Linux
> 8 and R 2.6.2, something funny happens: the characters
"overstrike"
> each other.  The Greek letter "mu" is printed several spaces to
the
> left of the "(" that it is supposed to follow.  I made an itty 
bitty
> picture of the figure title to show you:
>
> http://pj.freefaculty.org/R/plotmath_problem.png
>
> I can force in spaces to re-arrange the symbols so they do not
> overstrike. The following looks fine in the output.
>
>
> t1t2 <- bquote (paste("Normal (   ", mu== .(mu), '  , 
', sigma=> .(sigma)," )") )
> ### Note spaces manually inserted above are needed, otherwise plotmath
> overlaps "l" of
>
> plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)
>
>
> What do you suppose is wrong? The X configuration
My guess would be that something is wrong with the font metrics on one 
system. If the length of "Normal(" is miscalculated, that would
explain
the rest.

Do you see the same thing if you do something like

plot(0, main=quote(paste("Lengthy string", "A")))

It could be related to dpi settings; I seem to recall that this can do 
weird things on wide-screen displays. Doex xdpyinfo provide any clues? 
Look for lines like this

screen #0:
  dimensions:    1024x768 pixels (260x195 millimeters)
  resolution:    100x100 dots per inch
 
You could also play with the pointsize argument to X11() and see if the 
problem disappears at different sizes.

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907

Looks likes the the laptop is using different fonts with incorrect font 
metrics.  This could happen because it has a different screen resolution, 
or one of the systems is set to use scalable fonts or it is giving 
metrics for one fonts and using another or ....

BTW, this is probably nothing to do with plotmath per se -- the issue is 
most likely the device (presumably X11(), but you did not say) and its 
handling of font metric requests.  It looks to me as if the widths of 
normal text strings (and not symbols) is the problem.  I have seen 
something similar where there was a long-standing bug in plotmath (fixed 
in r44534), but this only manifested itself when text was kerned, which 
the X11() device in 2.6.2 does not ask for.

My best guess is that the font selected is (to use the technical terms) 
returning glyph widths without left/right bearings.

Please try 2.7.0 beta, which has a different X11() device (and the above 
bug fixed).  That ought to solve the problem for you, but otherwise you'll 
need to debug what the X11 metricInfo callback is giving you.

On Tue, 8 Apr 2008, Paul Johnson wrote:
> I've been testing plotmath.  But I'm getting some funny output one
one
> computer. The problem is that characters are 'jumbled' and
overstrike
> when symbols are introduced.
>
> Sample code:
>
> mu <- 440.0
> sigma <- 12.5
> myx <- seq( mu - 4*sigma,  mu+ 4*sigma, length.out=500)
> myDensity <- dnorm(myx,mean=mu,sd=sigma)
>
> # Here's one way to retrieve the values of mu and sigma and insert
> them into an expression
> t1t2 <- bquote (paste("Normal(", mu== .(mu), ',',
sigma== .(sigma),")") )
>
> plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)
>
>
> I have tested this code and it works on two desktop Fedora Linux 8
> systems to make a nice figure, but on a Dell Laptop with Fedora Linux
> 8 and R 2.6.2, something funny happens: the characters
"overstrike"
> each other.  The Greek letter "mu" is printed several spaces to
the
> left of the "(" that it is supposed to follow.  I made an itty 
bitty
> picture of the figure title to show you:
>
> http://pj.freefaculty.org/R/plotmath_problem.png
>
> I can force in spaces to re-arrange the symbols so they do not
> overstrike. The following looks fine in the output.
>
>
> t1t2 <- bquote (paste("Normal (   ", mu== .(mu), '  , 
', sigma=> .(sigma)," )") )
> ### Note spaces manually inserted above are needed, otherwise plotmath
> overlaps "l" of
>
> plot(myx, myDensity, type="l", xlab="X",
ylab="Probability Density ", main=t1t2)
>
>
> What do you suppose is wrong? The X configuration?
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595