Samo Jerom Samo Jerom - 1 month ago 26
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?

Answer

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

For your particular case:

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)

enter image description here