Hi list. I was saving my modified pairs graphic using a custom panel from
the R Graphics site, and I got an interesting difference in the final image
when I save it as eps or png.

This custom panel make possible to show at the left side of the pairs plot
the p-value as symbol and the correlation r value with its cex proportional
to the r value itself.

 

Well, when saving as a png file everything is pretty fine. But, if I save it
as an eps, one of the r values (0.0056) gets extremely bigger than it should
, and it's the only one presenting this behavior.

 

P.S.: I use GIMP 2.6.11 (x86) and GhostScript 9.00 (x86) to render the eps
file, I don't know if it could be an issue of one of these other softwares.

 

Below are the script that generates everything, a link to an example matrix
(csv) and a Sys.info result.

 

The link to an example data

 

http://dl.dropbox.com/u/2613625/Groups.csv

 

The script without the part used to import the data

 

# Analysis

cor.prob <- function(X, dfr = nrow(X) - 2) {

                R <- cor(X)

                above <- row(R) < col(R)

                r2 <- R[above]^2

                Fstat <- r2 * dfr / (1 - r2)

                R[above] <- 1 - pf(Fstat, 1, dfr)

                R

}

cor.prob(Grupos[,-7])

 

# Custom upper pairs panel

panel.cor <- function(x, y, digits=2, prefix="", cex.cor) 

{

    usr <- par("usr"); on.exit(par(usr)) 

    par(usr = c(0, 1, 0, 1)) 

    r <- abs(cor(x, y)) 

    txt <- format(c(r, 0.123456789), digits=digits)[1] 

    txt <- paste(prefix, txt, sep="") 

    if(missing(cex.cor)) cex <- 0.8/strwidth(txt) 

 

    test <- cor.test(x,y) 

    # borrowed from printCoefmat

    Signif <- symnum(test$p.value, corr = FALSE, na = FALSE, 

                  cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),

                  symbols = c("***", "**", "*", ".", " ")) 

 

    text(0.5, 0.5, txt, cex = cex * r) 

    text(.8, .8, Signif, cex=cex, col=2) 

}

 

# Saving the Graphics

postscript('CorMatrix.eps',paper='special',onefile=F,horizontal=F,bg='white'
,width=7,height=7,pointsize=9) # Here the issue pops up

par(pty='m')

pairs(Grupos[,-7],lower.panel=panel.smooth,upper.panel=panel.cor)

dev.off()

 

png('CorMatrix.png',bg='white',width=2800,height=2800,res=300) # Here
everything goes fine

par(pty='m')

pairs(Grupos[,-7],lower.panel=panel.smooth,upper.panel=panel.cor)

dev.off()

 

# System Information

Sys.info()

     sysname      release      version     nodename      machine
login 

   "Windows"      "7 x64" "build 7600" "RODRIGO-PC"     "x86-64"
"Rodrigo" 

        user 

   "Rodrigo"

 

Hope you can help me find out what is going on!

Regards

-------------------------------------------------------------------

MSc.  <mailto:r.aluizio@gmail.com> Rodrigo Aluizio


	[[alternative HTML version deleted]]

