Autoplot of PCA in R (Example)

In this tutorial, you’ll learn how to create a scatterplot and a biplot using the autoplot() function for Principal Component Analysis (PCA) results in the R programming language.

The table of content is structured as shown in the following box:

1) Load Libraries and Create Sample Data Set

2) Perform PCA

3) Scatterplot using autoplot()

4) Biplot using autoplot()

5) Video, Further Resources & Summary

Paula Villasante Soriano Statistician & R Programmer

This page was created in collaboration with Paula Villasante Soriano and Cansu Kebabci. Please have a look at Paula’s and Cansu’s author pages to get further information about their academic backgrounds and the other articles they have written for Statistics Globe.

Rana Cansu Kebabci Statistician & Data Scientist

Let’s start right away.

Load Libraries and Create Sample Data Set

Before we start, installing the libraries, ggplot2 and the ggfortify, is convenient.

install.packages("ggplot2")
install.packages("ggfortify")

If you have already installed these libraries in the past, just ignore this first step. Then skip to the following:

library(ggplot2)
library(ggfortify)

Next, we will call our sample data, which is a built-in dataset called iris in R.

data(iris)
head(iris)
# Sepal.Length Sepal.Width Petal.Length Petal.Width Species
# 1          5.1         3.5          1.4         0.2  setosa
# 2          4.9         3.0          1.4         0.2  setosa
# 3          4.7         3.2          1.3         0.2  setosa
# 4          4.6         3.1          1.5         0.2  setosa
# 5          5.0         3.6          1.4         0.2  setosa
# 6          5.4         3.9          1.7         0.4  setosa

Now, let’s perform our PCA using the sample data frame.

Perform PCA

In order to perform a PCA in R, we will choose all the columns except for the Species column since it is categorical. Hence, the first step is subsetting the dataset. For PCA designed for categorical variables, see our tutorial: Can PCA be Used for Categorical Variables?.

data <- iris[,1:4]
 
iris_pca <- prcomp(data, 
                 scale=TRUE)
summary(iris_pca)
#Importance of components:
#                           PC1    PC2     PC3     PC4
# Standard deviation     1.7084 0.9560 0.38309 0.14393
# Proportion of Variance 0.7296 0.2285 0.03669 0.00518
# Cumulative Proportion  0.7296 0.9581 0.99482 1.00000

Now, we can visualize our PCA results via the autoplot() function.

Scatterplot using autoplot()

All we need to visualize our PCA on a scatterplot using the autoplot() function is to input the iris_pca object to the function. If the users want to add a title and color the data points by group, they should also use the data, colour, and main arguments.

autoplot(iris_pca,
         data=iris,
         main = "Scatterplot",
         colour = 'Species')

Autoplot r pca

As seen, the axis labels specifying the principal components and explained variances (compare with the summary output of iris_pca) and the legend are added by default.

Biplot using autoplot()

We should use some additional function arguments to plot a biplot via autoplot(). First and foremost, loadings should be set to TRUE to make sure that one of the main visual components of biplots, loading vectors, are added. Then the rest is about how to color and label those vectors.

autoplot(iris_pca,
         data = iris,
         colour = 'Species',
         main = "Biplot", 
         loadings = TRUE,
         loadings.label=TRUE,
         loadings.colour = "black",
         loadings.label.colour="black",
         loadings.label.repel=TRUE)

Autoplot pca r colours

We hope you found this tutorial helpful. See you at the next one!

Video, Further Resources & Summary

Do you need more background on how to perform a Principal Component Analysis in R? Then check the following YouTube video of the Statistics Globe YouTube channel.

You could also have a look at some of the other tutorials available on Statistics Globe:

This post has shown how to make an autoplot of a PCA in R. In case you have any questions, you can leave a comment below.

8 Comments. Leave new

Alexandre
May 16, 2023 6:33 pm

Dear all, thank you very much for your collaborations.
I have a not-so-trivial question.
I would like to format the biplot variables in different ways. For example, the names Sepal.Width and Sepal.Length wanted the first to be Sepal subscribed Width and the other Sepal.Length in italics. Can someone help me?
Very grateful for the attention.
Yours sincerely,
Alexandre Jardim.

Reply
- Cansu (Statistics Globe)
  May 19, 2023 9:22 am
  Hello Alexandre,
  
  Renaming the variables is very easy using the names function. With that, you can rewrite Sepal.Width as Sepal_Width as follows.
  #rename data data(iris) names(iris)<-c("Sepal.Length", "Sepal_Width", "Petal.Length", "Petal.Width", "Species")
  Then you can perform PCA. As you said, labeling the vectors in italics is not trivial since autoplot() doesn’t provide a direct way to italicize loading labels. However, you can do it manually using the geom_segment and geom_text functions of ggplot2. See below.
  # load necessary libraries library(ggfortify) library(ggplot2) # perform PCA res.pca <- prcomp(iris[, -5], scale = TRUE) # get PCA plot for observations obs_plot <- autoplot(res.pca, loadings = FALSE) obs_plot # extract variable coordinates var.coord <- get_pca_var(res.pca)$coord var.coord # Add loadings to the plot final_plot <- obs_plot + geom_segment(data = as.data.frame(var.coord), aes(x = 0, y = 0, xend = 0.15*Dim.1, yend = 0.15*Dim.2), arrow = arrow(length = unit(0.15, "cm")), color="blue") + geom_text(data = as.data.frame(var.coord), aes(x = 0.15*Dim.1, y = 0.15*Dim.2, label = rownames(var.coord)), fontface = "italic", hjust = -0.1, vjust = 0.5) final_plot
  Please be aware that I rescaled the arrow lengths, which is done by default if you use the default settings of autoplot, to ensure that the arrows are visible in the graph. You can also try out other magnitudes to fit the labels better and use the just and just arguments for the adjustment. See the visual below.
  
  Regards,
  Cansu
  Reply
  - Alexandre
    May 19, 2023 12:11 pm
    
    Hello Cansu,
    Thank you very much for your contribution.
    Unfortunately, my problem has been partially resolved. I would really like my variable to be subscripted (i.e., SepalWidth).
    I tried using the tag but it didn’t work. Do you know of any solutions?
    Regards,
    Alexandre.
    
    Reply
    - Cansu (Statistics Globe)
      May 19, 2023 2:17 pm
      
      Hello Alexandre,
      
      You can easily change it by using the names function as I previously shared names(data)<-c("anyformat",...). If it doesn't answer your question, could you please give some examples for me to understand? Regards, Cansu
      
      Reply

Alexandre

May 19, 2023 7:03 pm

Dear Cansu,
I am very grateful that you have gone to great lengths to help me with this question.
Unfortunately, I still can’t solve my problem.
I am sending an image as I would like the variable names to be in the biplot.
https://i.im.ge/2023/05/20/hTLy8Y.Ex.png
Thanks again for all your help.
I hope you can help me.
Yours sincerely,
Alexandre.

Cansu (Statistics Globe)

May 22, 2023 8:16 am

Hello Alexander,

Thank you for the sample image. Creating a label variable using square brackets could help as follows. See the tutorial: Add Subscript and Superscript to Plot in R for further details. The general structure of the script is the same.

# load necessary libraries
library(ggfortify)
library(ggplot2)
 
# perform PCA
data(iris)
#rename data
data(iris)
names(iris)<-c("Sepal.Length", "Sepal_Width",  "Petal.Length", "Petal.Width",  "Species")
res.pca <- prcomp(iris[, -5], scale = TRUE)
 
# get PCA plot for observations
obs_plot <- autoplot(res.pca, loadings = FALSE)
 
# extract variable coordinates
var.coord <- get_pca_var(res.pca)$coord
 
# Create new labels
# Create new labels with subscript
new_labels <- c("Sepal.Width" = "Sepal[Width]", 
                "Sepal.Length" = "Sepal[Length]", 
                "Petal.Width" = "Petal[Width]", 
                "Petal.Length" = "Petal[Length]")
 
df<-as.data.frame(var.coord)
 
df$labels <- new_labels
 
# Add loadings to the plot
final_plot <- obs_plot + 
  geom_segment(data = df, 
               aes(x = 0, y = 0, xend = 0.1*Dim.1, yend = 0.1*Dim.2), 
               arrow = arrow(length = unit(0.2, "cm")), 
               color = "black", 
               inherit.aes = FALSE) +
  geom_text(data = df, 
            aes(x = 0.1*Dim.1, y = 0.1*Dim.2, label = labels), 
            parse = TRUE,  # parse mathematical expressions
            fontface = "italic", hjust = -0.1, vjust = 0.5, 
            inherit.aes = FALSE)
print(final_plot)

Regards,
Cansu

Alexandre
May 22, 2023 2:36 pm

Hi Cansu,
Thank you very much for your efficient response and your time dedicated to solving it.
My question was literally solved!
The work you do is fantastic, thank you very much.
All the best.
Regards,
Alexandre.

Reply
- Cansu (Statistics Globe)
  May 22, 2023 2:53 pm
  
  Hey Alexandre!
  
  Glad to hear that I could help!
  
  Best,
  Cansu
  
  Reply

Autoplot of PCA in R (Example)

Load Libraries and Create Sample Data Set

Perform PCA

Scatterplot using autoplot()

Biplot using autoplot()

Video, Further Resources & Summary

8 Comments. Leave new

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