I am trying to make a PCA plot with individuals -where one categorical variable (A) would be represented as the point shape (eg one group as a circle, a second one as a square, etc.) -and a second categorical variable (B) as the color inside the point Is that possible? Which code would you use?
1 Answers
I don't think you can modify the output from fviz_pca_ind(), so you would need to take out the data from the results, and plot it again using ggplot2:
library(factoextra)
library(ggplot2)
data <- iris
colnames(data)[5] <- "A"
data$B <- sample(letters[1:2],nrow(data),replace=TRUE)
res.pca <- prcomp(data[,1:4], scale = TRUE)
basic_plot <- fviz_pca_ind(res.pca, label="none")
ggplot(cbind(basic_plot$data,data[,c("A","B")]),
aes(x=x,y=y,col=A,shape=B)) + geom_point() + theme_bw()
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