
Launch RStudio as described here: Running RStudio and setting up your working directory

Prepare your data as described here: Best practices for preparing your data and save it in an external .txt tab or .csv files

Import your data into R
Data
iris data is used in the following examples. iris data set gives the measurements in centimeters of the variables sepal length and width, and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.
head(iris)
R base scatter plot matrices: pairs()
pairs(iris[,1:4], pch = 19)
pairs(iris[,1:4], pch = 19, lower.panel = NULL)
 Color points by groups (species)
my_cols < c("#00AFBB", "#E7B800", "#FC4E07")
pairs(iris[,1:4], pch = 19, cex = 0.5,
col = my_cols[iris$Species],
lower.panel=NULL)
 Add correlations on the lower panels: The size of the text is proportional to the correlations.
# Correlation panel
panel.cor < function(x, y){
usr < par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r < round(cor(x, y), digits=2)
txt < paste0("R = ", r)
cex.cor < 0.8/strwidth(txt)
text(0.5, 0.5, txt, cex = cex.cor * r)
}
# Customize upper panel
upper.panel<function(x, y){
points(x,y, pch = 19, col = my_cols[iris$Species])
}
# Create the plots
pairs(iris[,1:4],
lower.panel = panel.cor,
upper.panel = upper.panel)
 Add correlations on the scatter plots:
# Customize upper panel
upper.panel<function(x, y){
points(x,y, pch=19, col=c("red", "green3", "blue")[iris$Species])
r < round(cor(x, y), digits=2)
txt < paste0("R = ", r)
usr < par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
text(0.5, 0.9, txt)
}
pairs(iris[,1:4], lower.panel = NULL,
upper.panel = upper.panel)
Use the R package psych
The function pairs.panels [in psych package] can be also used to create a scatter plot of matrices, with bivariate scatter plots below the diagonal, histograms on the diagonal, and the Pearson correlation above the diagonal.
library(psych)
pairs.panels(iris[,5],
method = "pearson", # correlation method
hist.col = "#00AFBB",
density = TRUE, # show density plots
ellipses = TRUE # show correlation ellipses
)