Ok, I can replicate your problem, with following code:

dat <- 1:10
   barplot(dat, beside=TRUE,ylim=c(0,100));
   par()$usr;
   par(new=T);
   plot(dat, ylim=c(0,100), type="l");
   par()$usr;

So it looks like even if you specify yourself ylim, the resulting effective ylim (usr[3:4] ) will be different! More surprinsingly, setting the usr parameter before is not effective:
   par(new=T, usr=c(0,11,0,100));

this will not prevent    par()$usr; to be different than fixed :-(

No idea, but hopefully someone else on the list will be able to provide advice!

Matthieu




Le 19. 04. 11 20:47, John Kane a écrit :
What is Coredata(Z0)?
It would be very useful. as the posting guidelines suggest to supply working 
code and sample data.


--- On Tue, 4/19/11, Barbaglia, Guido (ESA)<guido.barbag...@fao.org>  wrote:

From: Barbaglia, Guido (ESA)<guido.barbag...@fao.org>
Subject: [R] Axes Alignment Problem for Multiple Plots
To: "r-help@r-project.org"<r-help@r-project.org>
Cc: "Stigler, Matthieu (EST)"<matthieu.stig...@fao.org>
Received: Tuesday, April 19, 2011, 11:42 AM
Dear all,

    I'm trying to plot, in the same window,
two different series, using barplot() for the first one and
plot() for the second. What happens is that the second chart
has a different axes origin, therefore the final plot is
wrong. This piece of code shows the differences between the
values of par()$usr:

    barplot(coredata(Z0), beside=TRUE,
ylim=c(0,100));
    par()$usr;
    par(new=T);
    plot(coredata(Z0), ylim=c(0,100));
    par()$usr;

I would like to know how it is possible to edit the values
of par()$usr[3:4] of the second chart in order to be the
same of the first one or, alternatively, how can I plot
together bar and line series within the same reference
system.


Best Regards
Guido Barbaglia
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