[R] Ternary Plots Do Not Display Ellipses in PDF

[David L Carlson]

I haven't looked at the source so I don't know exactly what is going on, but I think I have a work around. While running your example I noticed that ellipse() does not just add the ellipse to the plot produced by plot(), it replots the figure. However, just running ellipse() without plot() generates an error "Error in if (coorgeo == "acomp") { : argument is of length zero" so ellipse needs the plot environment produced by plot(). Moving the pdf() file works on my Windows machine:

> plot(winters.acomp, main="Winters Creek", cex=0.5)
> pdf("winters-pdf.pdf")
> ellipses(mean=mn, var=vr, r=r, steps=72, thinRatio=NULL, aspanel=FALSE,
+  col='red', lwd=2)
> dev.off()

-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352



-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Rich Shepard
Sent: Tuesday, October 14, 2014 4:21 PM
To: r-help at r-project.org
Subject: [R] Ternary Plots Do Not Display Ellipses in PDF

   A rather strange situation here and I've not found the source of the
problem.

   The point is to print a ternary plot matrix of compositional data with
ellipses enclosing 95% of the variance in each plot. The ellipses display on
the monitor, dev = x11cairo (see attached winters-x11cairo.pdf), but not when
sent directly to a file, dev = pdf (see attached winters-pdf.pdf).

   Here's winters.acomp:

structure(c(0.0666666666666667, 0.0612244897959184, 0.0434782608695652, 
0.043956043956044, 0.05, 0.0161290322580645, 0.6, 0.571428571428571, 
0.623188405797101, 0.593406593406593, 0.433333333333333, 0.629032258064516,
0.0666666666666667, 0.0612244897959184, 0.101449275362319, 0.0659340659340659, 
0.0666666666666667, 0.032258064516129, 0.244444444444444, 0.26530612244898,
0.217391304347826, 0.263736263736264, 0.366666666666667, 0.290322580645161,
0.0222222222222222, 0.0408163265306122, 0.0144927536231884, 0.032967032967033, 
0.0833333333333333, 0.032258064516129), .Dim = c(6L, 5L), .Dimnames = list(
     NULL, c("filter", "gather", "graze", "predate", "shred")), class = "acomp")

   And this is the command sequence:

> library(compositions)
> plot(winters.acomp, main="Winters Creek", cex=0.5)
> r <- sqrt(qchisq(p=0.95, df=4))
> mn <- mean(winters.acomp)
> vr <- var(winters.acomp)
> plot(winters.acomp, main="Winters Creek", cex=0.5)
> ellipses(mean=mn, var=vr, r=r, steps=72, thinRatio=NULL, aspanel=FALSE,
 	col='red', lwd=2)
# monitor plot window is manually closed.
> pdf("winters-pdf.pdf")
> plot(winters.acomp, main="Winters Creek", cex=0.5)
> ellipses(mean=mn, var=vr, r=r, steps=72, thinRatio=NULL, aspanel=FALSE,
 	col='red', lwd=2)
> dev.off()

   What am I not seeing here that causes the different outputs?

Rich