number of observations used in scatterplot.matrix()
Maria, You can have number of complete pairs for each column pair combination as (x <- matrix(c(NA,NA,NA,1,2,3), 2, 3)) (x.na <- !is.na(x)) t(x.na) %*% x.na You can supply this as is or its lower triangle as vector to the plotting function. Cheers, Peter On Fri, Jan 21, 2011 at 8:25 AM, Maria Dulce Subida
<mdsubida at icman.csic.es> wrote:
Hi Luciano, Thank you for your suggestion. However I'm afraid it will not work, since the actual number of observations used by cor.test() is not the total number of observations (nrow(x)) ?I have. cor.test() omits observations with NAs in x or in y, which do actually occur in my data sets. Kind regards, Dulce El 21/01/2011 16:13, Luciano Selzer escribi?:
Hi, maybe something like this should do the trick:
? ? ? ? ? n <- nrow(x)
? ? ? ? ? ? txt <- paste("rho=", txt, "\np=",pval, "n=", n, sep="")
HTH
Luciano
2011/1/21 Maria Dulce Subida <mdsubida at icman.csic.es
<mailto:mdsubida at icman.csic.es>>
? ? Dear all,
? ? I have a script (please see below) that gives a scatter plot matrix on
? ? the upper panel, and the spearman rho and probability values on the
? ? lower panel. It also gives the density function of each variable
? ? in the
? ? diagonal, adds a smoother and a linear regression line to each scatter
? ? plot, and puts significant spearman coefficient values in red.
? ? Now I would like to add to the lower panel information, the value of
? ? n=number of observations used to calculate the spearman correlation
? ? coefficient. Does anyone know I could I add that parameter to my
? ? function panel.cor?
? ? Thank you!
? ? Kind regards,
? ? Dulce
? ? ################
? ? panel.cor <- function (x, y,method="spearman",digits=2,...)
? ? {
? ? ? ? ? ? points(x,y,type="n");
? ? ? ? ? ? usr <- par("usr"); on.exit(par(usr))
? ? ? ? ? ? par(usr = c(0, 1, 0, 1));
? ? ? ? ? ? correl <- cor.test(x, y,method=method);
? ? ? ? ? ? r=correl$estimate;
? ? ? ? ? ? pval=correl$p.value;
? ? ? ? ? ? color="black";
? ? ? ? ? ? if (pval<0.05) color="red";
? ? ? ? ? ? txt <- format(r,digits=2)
? ? ? ? ? ? pval <- format(pval,digits=2)
? ? ? ? ? ?n <- nrow(x)
? ? ? ? ? ? txt <- paste("rho=", txt, "\np=",pval, "n=", n, sep="")
? ? ? ? ? ? text(0.5, 0.5, txt,col=color)
? ? }
? ? scatterplot.matrix (~ var1 + var2 + var3 , data=mydata,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? main="Mydata", smooth=TRUE,
? ? lower.panel=panel.cor, pch=20, cex=0.5,
? ? col=c("red","black"),cex.labels=1, font.labels=2, lwd=0.5)
? ? ? ? ? ?[[alternative HTML version deleted]]
? ? _______________________________________________
? ? R-sig-ecology mailing list
? ? R-sig-ecology at r-project.org <mailto:R-sig-ecology at r-project.org>
? ? https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology