# Five ways to visualize your pairwise comparisons

**Recology**, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)

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In data analysis it is often nice to look at all pairwise combinations of continuous variables in scatterplots. Up until recently, I have used the function splom in the package lattice, but ggplot2 has superior aesthetics, I think anyway.

Here a few ways to accomplish the task:

# load packages

require(lattice) require(ggplot2)

1) Using base graphics, function “pairs”

pairs(iris[1:4], pch = 21)

2) Using lattice package, function “splom”

splom(~iris[1:4])

3) Using package ggplot2, function “plotmatrix”

plotmatrix(iris[1:4])

4) a function called ggcorplot by Mike Lawrence at Dalhousie University

-get ggcorplot function at this link

ggcorplot( data = iris[1:4], var_text_size = 5, cor_text_limits = c(5,10))

5) panel.cor function using pairs, similar to ggcorplot, but using base graphics. Not sure who wrote this function, but here is where I found it.

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) } pairs(iris[1:4], lower.panel=panel.smooth, upper.panel=panel.cor)

A comparison of run times...

> system.time(pairs(iris[1:4])) user system elapsed 0.138 0.008 0.156 > system.time(splom(~iris[1:4])) user system elapsed 0.003 0.000 0.003 > system.time(plotmatrix(iris[1:4])) user system elapsed 0.052 0.000 0.052 > system.time(ggcorplot( + data = iris[1:4], var_text_size = 5, cor_text_limits = c(5,10))) user system elapsed 0.130 0.001 0.131 > system.time(pairs(iris[1:4], lower.panel=panel.smooth, upper.panel=panel.cor)) user system elapsed 0.170 0.011 0.200

...shows that splom is the fastest method, with the method using the panel.cor function pulling up the rear.

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**Recology**.

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