[R] several postscript problems

[Richard.Cotton at hsl.gov.uk]

> I'm currently trying to export a couple of graphs to pdf . Postscript 
> would be fine too, but I'm using odd page dimensions, which seem to be 
> overwritten when using the "ps2pdf" command. I'm using the pdfpages 
> package in LaTeX to put 6 graphs onto one page (this is why it ought to 
> be a pdf in the end).
> 
> I have two problems:
> 
> 1. I'm using "arrows" to add error bars to the plots and they come out 
> all misplaced. I've read in older posts that this might be solved using 
> Acrobat Reader, but would this mean that I have to teach LaTeX (Lyx) 
> somehow to use Acrobat too?
> 
> 2. I'm also using a legend that includes some dots (pch=1, pch=19), 
> which pdf obviously doesn't understand and plots little q symbols 
> instead (postscript will understand these symbols). Do I have to load a 
> certain font to get it to work?

> Examples:
> R:                pdf("result.pdf",height=4,width=4)
> ...
> ### plot empty window
>    plot(0,0, type="n", ylim=c(-180,180), xlim=c(0,0.5), xlab="", 
> ylab="Phase", xaxt="n", yaxt="n")
>    axis(1,at=seq(0,0.5,0.1),label=rep(" ",6))
>    axis(2,at=seq(-180,180,90))
>    abline(h=0,lty=3)
>    legend("topright",c("annual means", "summer 
means"),pch=c(19,1),cex=1)
> 
> ### plot with error bars in loop
> plot(get(site[j,i])[k,1],get(site[j,i])[k,3],pch=19,axes=F,ann=F,
> ylim=c(-180,180),xlim=c(0,0.5),col=plotcolour[i])
> arrows(get(site[j,i])[k,1],get(site[j,i])[k,3]+get(site[j,i])[k,4],
> get(site[j,i])[k,1],get(site[j,i])[k,3]-get(site[j,i])[k,4],length 
> = .03, angle = 90, code = 3,col=plotcolour[i])
> ...
> dev.off()

In order to solve this, you need to work out if the problem is with R, or 
with Latex.  Try creating a pdf, and viewing that directly, without 
incorporating it into a Latex document.  You may also want to try some 
simpler plots, to check that you can display the correct pch figures and 
arrows properly.

Test 1
plot(1:10, pch=c(1,19)) 
Do the dots display okay?

Test 2
pdf("test2.pdf")
plot(1:10, pch=c(1,19))
dev.off()
Are they still okay?

Test 3
pdf("test3.pdf")
plot(1:10)
arrows(10,1,1,10)
dev.off()
Is the arrow in the right place?

Test 4
Plot your more complex figure on screen, is it all okay?

Test 5
Now write to pdf.

Test 6 
Now incorporate into Latex doc.

Regards,
Richie.

Mathematical Sciences Unit
HSL


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