Corrplot correlation configuration

Question

I'm new to R scripts :-)

I need to build a correlation matrix, and I'm trying to adjust some parameters to adapt the graph. I am using the corrplot package.

I built the 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 to show the correlation values ​​in the lower matrix inside the color matrix I built. How can i do this?

Is it possible to exclude the main diagonal from the lower matrix? In this diagonal, we always have the perfect ratio.

Another doubt is that I want to show significant values ​​for correlation using stars instead of squares. be in love (*,, *). Is it possible?

Can you help me guys?

Answer 1

With a bit of hacking, you can do this in a very similar R package, corrgram . This allows you to easily define your own panel functions and helps you easily view them as templates. Here the code and the figure appeared:

 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 is not very clean, as it basically fixes the functions from the package, but it should give you a good start to get the plot you want. Perhaps you can also use a similar approach with the corrplot package.

update: Here is the version with stars and cor in 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 on another way to show significance, it will be bold over the threshold, and not using stars. Perhaps this will be clearer, depending on what you want to show.