Correlation Corrplot Configuration

Question

I am newbie in R scripts :-)

I need build a correlation matrix and I´am trying to configurate some parameters to adapt the graph. I am using the corrplot package.

I Built a corrplot matrix this way:

corrplot(cor(d1[,2:14], d1[,2:14]), method=c("color"),
         bg = "white", addgrid.col = "gray50", 
         tl.cex=1, type="lower", tl.col = "black", 
         col = colorRampPalette(c("red","white","blue"))(100))

I need show the values of correlation in the lower matrix inside the color matrix that I built. How i can do that?

Is it possible exclude the main diagonal from the lower matrix? In this diagonl always we have the perfect correlation.

The other doubt - I want to show the significant values for the correlation using stars instead of squares. like (*, , *). Is it possible?

Can you help me guys?

Boisterous

Could lower.tri function be helpful? Take a look at ?lower.tri – Suctorial

Answer 1

With a bit of hackery you can do this in a very similar R package, corrgram. This one allows you to easily define your own panel functions, and helpfully makes theirs easy to view as templates. Here's the some code and figure produced:

set.seed(42)
library(corrgram)

# This panel adds significance starts, or NS for not significant
panel.signif <-  function (x, y, corr = NULL, col.regions, digits = 2, cex.cor, 
                           ...) {
  usr <- par("usr")
  on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  results <- cor.test(x, y, alternative = "two.sided")
  est <- results$p.value
  stars <- ifelse(est < 5e-4, "***", 
                  ifelse(est < 5e-3, "**", 
                         ifelse(est < 5e-2, "*", "NS")))
  cex.cor <- 0.4/strwidth(stars)
  text(0.5, 0.5, stars, cex = cex.cor)
}

# This panel combines edits the "shade" panel from the package
# to overlay the correlation value as requested
panel.shadeNtext <- function (x, y, corr = NULL, col.regions, ...) 
{
  if (is.null(corr)) 
    corr <- cor(x, y, use = "pair")
  ncol <- 14
  pal <- col.regions(ncol)
  col.ind <- as.numeric(cut(corr, breaks = seq(from = -1, to = 1, 
                                               length = ncol + 1), include.lowest = TRUE))
  usr <- par("usr")
  rect(usr[1], usr[3], usr[2], usr[4], col = pal[col.ind], 
       border = NA)
  box(col = "lightgray")
  on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  r <- formatC(corr, digits = 2, format = "f")
  cex.cor <- .8/strwidth("-X.xx")
  text(0.5, 0.5, r, cex = cex.cor)
}

# Generate some sample data
sample.data <- matrix(rnorm(100), ncol=10)

# Call the corrgram function with the new panel functions
# NB: call on the data, not the correlation matrix
corrgram(sample.data, type="data", lower.panel=panel.shadeNtext, 
         upper.panel=panel.signif)

The code isn't very clean, as it's mostly patched together functions from the package, but it should give you a good start to get the plot you want. Possibly you can take a similar approach with the corrplot package too.

update: Here's a version with stars and cor on the same triangle:

panel.shadeNtext <- function (x, y, corr = NULL, col.regions, ...) 
{
  corr <- cor(x, y, use = "pair")
  results <- cor.test(x, y, alternative = "two.sided")
  est <- results$p.value
  stars <- ifelse(est < 5e-4, "***", 
                  ifelse(est < 5e-3, "**", 
                         ifelse(est < 5e-2, "*", "")))
  ncol <- 14
  pal <- col.regions(ncol)
  col.ind <- as.numeric(cut(corr, breaks = seq(from = -1, to = 1, 
                                               length = ncol + 1), include.lowest = TRUE))
  usr <- par("usr")
  rect(usr[1], usr[3], usr[2], usr[4], col = pal[col.ind], 
       border = NA)
  box(col = "lightgray")
  on.exit(par(usr))
  par(usr = c(0, 1, 0, 1))
  r <- formatC(corr, digits = 2, format = "f")
  cex.cor <- .8/strwidth("-X.xx")
  fonts <- ifelse(stars != "", 2,1)
  # option 1: stars:
  text(0.5, 0.4, paste0(r,"\n", stars), cex = cex.cor)
  # option 2: bolding:
  #text(0.5, 0.5, r, cex = cex.cor, font=fonts)
}

# Generate some sample data
sample.data <- matrix(rnorm(100), ncol=10)

# Call the corrgram function with the new panel functions
# NB: call on the data, not the correlation matrix
corrgram(sample.data, type="data", lower.panel=panel.shadeNtext, 
         upper.panel=NULL)

Also commented out is another way of showing significance, it'll bold those below a threshold rather than using stars. Might be clearer that way, depending on what you want to show.

Belcher

Hi.. @Belcher Is it possible to put stars together as the correlacion value in a squares and use only the half matrix? – Boisterous

Yes I've updated my answer with an example of how you can do that, hope that helps – Belcher

its easy add a legend for the colors? like my firts example. So thank you!!! You help me a lot! @Belcher :-) – Boisterous

It's not implemented in the corrgram package but you can make one yourself, the source of the above functions show how the colours are generated. Investigate what's going on and if you can't figure it out then maybe ask a new question. The colours and correlations are showing the same data though, so a legend isn't all that necessary – Belcher