Analysis in R: PCA results in ggplot2 displayed in Biplot “ggbiplot” package

This is an introduction to the ggplot2 package for displaying the results of a principal component analysis in Biplot.

Package version is 0.55. Checked with R version 4.1.2.

Install Package

Run the following command.

#Install Package
install.packages("devtools")
devtools::install_github("vqv/ggbiplot")

Examples

See the command and package help for details.

#Loading the library
library("ggbiplot")

###Creating Data#####
set.seed(1234)
TestData <- matrix(rnorm(1000), 200)
TestData <- as.data.frame(TestData)
#Data Adjustment
TestData[1:67,] <- TestData[1:67,] + 1
TestData[68:135,] <- TestData[68:135,] + 2
TestData[136:200,] <- TestData[136:200,] + 3
#Group information is assigned
TestData <- cbind(c(rep("Group1", 67),
                    rep("Group2", 67),
                    rep("Group3", 66)),
                  TestData)
colnames(TestData) <- c("Group", paste0("ColName", seq(5)))
########

#stat package:Principal component analysis with prcomp command
TestPrc <- prcomp(TestData[, 2:6], scale. = FALSE)

#Create biplot:ggbiplot command
#Specifies the result of prcomp() or princomp():pcobj option
#The principal component to be plotted:choices option
#Group Information:groups option
#Probability ellipses for each group:ellipse option
#Describes a correlated circle:circle option
#The command ggplot2 is available
ggbiplot(pcobj = TestPrc, choices = 1:2, obs.scale = 1, var.scale = 1,
         groups = TestData[, 1], ellipse = TRUE, circle = TRUE) +
  scale_colour_manual(values = c("#FF0000", "black", "#00FF00")) +
  theme(legend.direction = "horizontal", legend.position = "top")

Output Examples

・ggbiplot command

I hope this makes your analysis a little easier !!