How to highlight a particular variable or individual in a PCA space in R-CodePudding

I am currently working on a large dataset (count data with species x samples) from which I performed a PCA. What I get is a massive cloud of points, and I would like to color one given species to show where it is located in this cloud (species are my variables here). Here is what it looks like :

I use the package factoextra, and visualize the variables with fviz_pca_var. Is there a way to select one particular species and display it with a color different than the others ?

Thank you for your help

CodePudding user response：

If it's just a single point you want to color, perhaps:

library(tidyverse)
library(factoextra)
library(FactoMineR)

data("iris")

iris$assigned_colors <- NA
# Change the color of the 'individual of interest'
iris[9,]$assigned_colors <- "red"

iris.pca <- PCA(iris[,-c(5,6)], graph = FALSE)

fviz_pca_ind(iris.pca,
             geom = "point",
             geom.ind = "point")  
  geom_point(aes(color = iris$assigned_colors))  
  scale_color_identity()
#> Warning: Removed 149 rows containing missing values (geom_point).

^{Created on 2022-07-08 by the}