Samo Jerom - 1 year ago 133
R Question

# How to modify this Correlation Matrix plot?

I have the following codes to display a correlation matrix,

``````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(USJudgeRatings[,c(2:3,6,1,7)],
lower.panel=panel.smooth, upper.panel=panel.cor)
``````

I want to modify the plot like:

1. Have smaller blue dots as

``````pairs(USJudgeRatings[,c(2:3,6,1,7)],
main="xxx",
pch=18,
col="blue",
cex=0.8)
``````

2. Include a histogram of the entries on the diagonal (as seen in enter link description here)

3. Display the correlation and p-value as

``````r=0.9;
p=0.001;
``````

with values not stars.

There is a fitting line displayed for the scatter plot of the paired data. What is the method used for the fitting? Which line is defined the fitting as the codes shown above? And how to change the fitting method?

Help page for the function `pairs()` gives you example how to define panels to plot.

Changed `panel.cor()` function to show to lines of text - p-values and correlation coefficients.

``````panel.cor <- function(x, y, digits=2, 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]
test <- cor.test(x,y)
Signif <- ifelse(round(test\$p.value,3)<0.001,"p<0.001",paste("p=",round(test\$p.value,3)))
text(0.5, 0.25, paste("r=",txt))
text(.5, .75, Signif)
}
``````

For `panel.smooth()` function defined `cex=`, `col=` and `pch=` arguments.

``````panel.smooth<-function (x, y, col = "blue", bg = NA, pch = 18,
cex = 0.8, col.smooth = "red", span = 2/3, iter = 3, ...)
{
points(x, y, pch = pch, col = col, bg = bg, cex = cex)
ok <- is.finite(x) & is.finite(y)
if (any(ok))
lines(stats::lowess(x[ok], y[ok], f = span, iter = iter),
col = col.smooth, ...)
}
``````

To add histograms, `panel.hist()` functions should be defined (taken from help file of `pairs()`)

``````panel.hist <- function(x, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h <- hist(x, plot = FALSE)
breaks <- h\$breaks; nB <- length(breaks)
y <- h\$counts; y <- y/max(y)
rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
}
``````

Final plot:

``````pairs(USJudgeRatings[,c(2:3,6,1,7)],
lower.panel=panel.smooth, upper.panel=panel.cor,diag.panel=panel.hist)
``````

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