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Principal Component Analysis in R: prcomp vs princomp
&  kassambara |  ' 08/10/2017 |  ( 412083  | ) Comments (4)  | * Principal Component Methods in R: Practical Guide
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by FeedBurner This R tutorial describes how to perform a Principal Component Analysis (PCA) using the built-in R functions prcomp()
and princomp(). You will learn how to predict new individuals and variables coordinates using PCA. We’ll also provide
the theory behind PCA results.
on Social Networks
Learn more about the basics and the interpretation of principal component analysis in our previous article: PCA -
Principal Component Analysis Essentials.

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resources to help you on your
path...

Contents:

General methods for principal component analysis

prcomp() and princomp() functions
Package for PCA visualization
Demo data sets
Compute PCA in R using prcomp()
Access to the PCA results
Predict using PCA
Supplementary individuals
Supplementary variables

Theory behind PCA results

PCA results for variables
PCA results for individuals

Related Book:

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General methods for principal component analysis

There are two general methods to perform PCA in R :

Spectral decomposition which examines the covariances / correlations between variables

Singular value decomposition which examines the covariances / correlations between individuals

The function princomp() uses the spectral decomposition approach. The functions prcomp() and PCA()[FactoMineR]
use the singular value decomposition (SVD).

+ According to the R help, SVD has slightly better numerical accuracy. Therefore, the function prcomp() is pre-
ferred compared to princomp().

prcomp() and princomp() functions

The simplified format of these 2 functions are :

prcomp(x, scale = FALSE)

princomp(x, cor = FALSE, scores = TRUE)

1. Arguments for prcomp():

x: a numeric matrix or data frame

scale: a logical value indicating whether the variables should be scaled to have unit variance before the analysis
takes place

2. Arguments for princomp():

x: a numeric matrix or data frame

cor: a logical value. If TRUE, the data will be centered and scaled before the analysis
scores: a logical value. If TRUE, the coordinates on each principal component are calculated

The elements of the outputs returned by the functions prcomp() and princomp() includes :

prcomp() name princomp() name Description

Course & Specialization
sdev sdev the standard deviations of the principal components
Recommended for You (on
Coursera): rotation loadings the matrix of variable loadings (columns are eigenvectors)
Course: Machine
Learning: Master the center center the variable means (means that were substracted)
Fundamentals
Specialization: Data scale scale the variable standard deviations (the scaling applied to each variable )
Science
The coordinates of the individuals (observations) on the principal com-
Specialization: Python x scores
ponents.
for Everybody
Course: Build Skills for a
Top Job in any Industry
Specialization: Master
, In the following sections, we’ll focus only on the function prcomp()
Machine Learning
Fundamentals
Specialization: Statistics Package for PCA visualization
with R
Specialization: Software We’ll use the factoextra R package to create a ggplot2-based elegant visualization.
Development in R
Specialization: Genomic You can install it from CRAN:
Data Science
install.packages("factoextra")

See More Resources

Or, install the latest developmental version from github:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/factoextra")

Load factoextra as follow:

library(factoextra)

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Demo data sets

analyzing data We’ll use the data sets decathlon2 [in factoextra], which has been already described at: PCA - Data format.

Briefly, it contains:
pca analysis
Active individuals (rows 1 to 23) and active variables (columns 1 to 10), which are used to perform the principal
data extraction component analysis
Supplementary individuals (rows 24 to 27) and supplementary variables (columns 11 to 13), which coordinates will
be predicted using the PCA information and parameters obtained with active individuals/variables.
factor analysis

spss analysis

R Packages

factoextra

survminer

ggpubr

ggcorrplot

fastqcr

Gagnez 30
Go de
bonus
Load the data and extract only active individuals and variables:
internet
Optez pour le library("factoextra")
data(decathlon2)
Smartbox 4G
decathlon2.active <- decathlon2[1:23, 1:10]
de Airtel et head(decathlon2.active[, 1:6])
gagnez 30 Go
de bonus
internet. ## X100m Long.jump Shot.put High.jump X400m X110m.hurdle
## SEBRLE 11.0 7.58 14.8 2.07 49.8 14.7
## CLAY 10.8 7.40 14.3 1.86 49.4 14.1
Airtel ## BERNARD 11.0 7.23 14.2 1.92 48.9 15.0
## YURKOV 11.3 7.09 15.2 2.10 50.4 15.3
Madagascar ## ZSIVOCZKY 11.1 7.30 13.5 2.01 48.6 14.2
## McMULLEN 10.8 7.31 13.8 2.13 49.9 14.4

Ouvrir Compute PCA in R using prcomp()

In this section we’ll provide an easy-to-use R code to compute and visualize PCA in R using the prcomp() function and
the factoextra package.

1. Load factoextra for visualization

Our Books
library(factoextra)

2. Compute PCA

res.pca <- prcomp(decathlon2.active, scale = TRUE)

3. Visualize eigenvalues (scree plot). Show the percentage of variances explained by each principal component.

R Graphics Essentials for

Great Data Visualization:

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200 Practical Examples

You Want to Know for fviz_eig(res.pca)
Data Science
⋆ NEW!!

Practical Guide to Cluster

Analysis in R

Practical Guide to
Principal Component
Methods in R

3D Plots in R 4. Graph of individuals. Individuals with a similar profile are grouped together.

fviz_pca_ind(res.pca,
col.ind = "cos2", # Color by the quality of representation
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
repel = TRUE # Avoid text overlapping
)

Gagnez
30 Go de
bonus
internet
Airtel Madagascar

Optez pour le
Smartbox 4G
de Airtel et
gagnez 30 Go
de bonus
5. Graph of variables. Positive correlated variables point to the same side of the plot. Negative correlated variables
internet. point to opposite sides of the graph.

fviz_pca_var(res.pca,
col.var = "contrib", # Color by contributions to the PC
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
OUVRIR repel = TRUE # Avoid text overlapping
)

Blogroll

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Datanovia: Online
Data Science Courses

R-Bloggers

6. Biplot of individuals and variables

fviz_pca_biplot(res.pca, repel = TRUE,

col.var = "#2E9FDF", # Variables color
col.ind = "#696969" # Individuals color
)

Access to the PCA results

library(factoextra)
# Eigenvalues
eig.val <- get_eigenvalue(res.pca)
eig.val

# Results for Variables

res.var <- get_pca_var(res.pca)
res.var$coord # Coordinates
res.var$contrib # Contributions to the PCs

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res.var$cos2 # Quality of representation

# Results for individuals
res.ind <- get_pca_ind(res.pca)
res.ind$coord # Coordinates
res.ind$contrib # Contributions to the PCs
res.ind$cos2 # Quality of representation

Predict using PCA

In this section, we’ll show how to predict the coordinates of supplementary individuals and variables using only the in-
formation provided by the previously performed PCA.

Supplementary individuals
1. Data: rows 24 to 27 and columns 1 to to 10 [in decathlon2 data sets]. The new data must contain columns (vari-
ables) with the same names and in the same order as the active data used to compute PCA.

# Data for the supplementary individuals

ind.sup <- decathlon2[24:27, 1:10]
ind.sup[, 1:6]

## X100m Long.jump Shot.put High.jump X400m X110m.hurdle

## KARPOV 11.0 7.30 14.8 2.04 48.4 14.1
## WARNERS 11.1 7.60 14.3 1.98 48.7 14.2
## Nool 10.8 7.53 14.3 1.88 48.8 14.8
## Drews 10.9 7.38 13.1 1.88 48.5 14.0

2. Predict the coordinates of new individuals data. Use the R base function predict():

ind.sup.coord <- predict(res.pca, newdata = ind.sup)

ind.sup.coord[, 1:4]

## PC1 PC2 PC3 PC4

## KARPOV 0.777 -0.762 1.597 1.686
## WARNERS -0.378 0.119 1.701 -0.691
## Nool -0.547 -1.934 0.472 -2.228
## Drews -1.085 -0.017 2.982 -1.501

3. Graph of individuals including the supplementary individuals:

# Plot of active individuals

p <- fviz_pca_ind(res.pca, repel = TRUE)
# Add supplementary individuals
fviz_add(p, ind.sup.coord, color ="blue")

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The predicted coordinates of individuals can be manually calculated as follow:

1. Center and scale the new individuals data using the center and the scale of the PCA
2. Calculate the predicted coordinates by multiplying the scaled values with the eigenvectors (loadings) of the princi-
pal components.

The R code below can be used :

# Centering and scaling the supplementary individuals

ind.scaled <- scale(ind.sup,
center = res.pca$center,
scale = res.pca$scale)
# Coordinates of the individividuals
coord_func <- function(ind, loadings){
r <- loadings*ind
apply(r, 2, sum)
}
pca.loadings <- res.pca$rotation
ind.sup.coord <- t(apply(ind.scaled, 1, coord_func, pca.loadings ))
ind.sup.coord[, 1:4]

## PC1 PC2 PC3 PC4

## KARPOV 0.777 -0.762 1.597 1.686
## WARNERS -0.378 0.119 1.701 -0.691
## Nool -0.547 -1.934 0.472 -2.228
## Drews -1.085 -0.017 2.982 -1.501

Supplementary variables

Qualitative / categorical variables

The data sets decathlon2 contain a supplementary qualitative variable at columns 13 corresponding to the type of com-
petitions.

Qualitative / categorical variables can be used to color individuals by groups. The grouping variable should be of same
length as the number of active individuals (here 23).

groups <- as.factor(decathlon2$Competition[1:23])

fviz_pca_ind(res.pca,
col.ind = groups, # color by groups
palette = c("#00AFBB", "#FC4E07"),
addEllipses = TRUE, # Concentration ellipses
ellipse.type = "confidence",
legend.title = "Groups",
repel = TRUE
)

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Calculate the coordinates for the levels of grouping variables. The coordinates for a given group is calculated as the
mean coordinates of the individuals in the group.

library(magrittr) # for pipe %>%

library(dplyr) # everything else
# 1. Individual coordinates
res.ind <- get_pca_ind(res.pca)
# 2. Coordinate of groups
coord.groups <- res.ind$coord %>%
as_data_frame() %>%
select(Dim.1, Dim.2) %>%
mutate(competition = groups) %>%
group_by(competition) %>%
summarise(
Dim.1 = mean(Dim.1),
Dim.2 = mean(Dim.2)
)
coord.groups

## # A tibble: 2 x 3
## competition Dim.1 Dim.2
##
## 1 Decastar -1.31 -0.119
## 2 OlympicG 1.20 0.109

Quantitative variables
Data: columns 11:12. Should be of same length as the number of active individuals (here 23)

quanti.sup <- decathlon2[1:23, 11:12, drop = FALSE]

head(quanti.sup)

## Rank Points
## SEBRLE 1 8217
## CLAY 2 8122
## BERNARD 4 8067
## YURKOV 5 8036
## ZSIVOCZKY 7 8004
## McMULLEN 8 7995

The coordinates of a given quantitative variable are calculated as the correlation between the quantitative variables and
the principal components.

# Predict coordinates and compute cos2

quanti.coord <- cor(quanti.sup, res.pca$x)
quanti.cos2 <- quanti.coord^2

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# Graph of variables including supplementary variables

p <- fviz_pca_var(res.pca)
fviz_add(p, quanti.coord, color ="blue", geom="arrow")

Theory behind PCA results

PCA results for variables

Here we’ll show how to calculate the PCA results for variables: coordinates, cos2 and contributions:

var.coord = loadings * the component standard deviations

var.cos2 = var.coord^2
var.contrib. The contribution of a variable to a given principal component is (in percentage) : (var.cos2 * 100) /
(total cos2 of the component)

# Helper function
#::::::::::::::::::::::::::::::::::::::::
var_coord_func <- function(loadings, comp.sdev){
loadings*comp.sdev
}
# Compute Coordinates
#::::::::::::::::::::::::::::::::::::::::
loadings <- res.pca$rotation
sdev <- res.pca$sdev
var.coord <- t(apply(loadings, 1, var_coord_func, sdev))
head(var.coord[, 1:4])

## PC1 PC2 PC3 PC4

## X100m -0.851 0.1794 -0.302 0.0336
## Long.jump 0.794 -0.2809 0.191 -0.1154
## Shot.put 0.734 -0.0854 -0.518 0.1285
## High.jump 0.610 0.4652 -0.330 0.1446
## X400m -0.702 -0.2902 -0.284 0.4308
## X110m.hurdle -0.764 0.0247 -0.449 -0.0169

# Compute Cos2
#::::::::::::::::::::::::::::::::::::::::
var.cos2 <- var.coord^2
head(var.cos2[, 1:4])

## PC1 PC2 PC3 PC4

## X100m 0.724 0.032184 0.0909 0.001127
## Long.jump 0.631 0.078881 0.0363 0.013315
## Shot.put 0.539 0.007294 0.2679 0.016504

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## High.jump 0.372 0.216424 0.1090 0.020895

## X400m 0.492 0.084203 0.0804 0.185611
## X110m.hurdle 0.584 0.000612 0.2015 0.000285

# Compute contributions
#::::::::::::::::::::::::::::::::::::::::
comp.cos2 <- apply(var.cos2, 2, sum)
contrib <- function(var.cos2, comp.cos2){var.cos2*100/comp.cos2}
var.contrib <- t(apply(var.cos2,1, contrib, comp.cos2))
head(var.contrib[, 1:4])

## PC1 PC2 PC3 PC4

## X100m 17.54 1.7505 7.34 0.1376
## Long.jump 15.29 4.2904 2.93 1.6249
## Shot.put 13.06 0.3967 21.62 2.0141
## High.jump 9.02 11.7716 8.79 2.5499
## X400m 11.94 4.5799 6.49 22.6509
## X110m.hurdle 14.16 0.0333 16.26 0.0348

PCA results for individuals

ind.coord = res.pca$x
Cos2 of individuals. Two steps:
Calculate the square distance between each individual and the PCA center of gravity: d2 = [(var1_ind_i -
mean_var1)/sd_var1]^2 + …+ [(var10_ind_i - mean_var10)/sd_var10]^2 + …+..
Calculate the cos2 as ind.coord^2/d2

Contributions of individuals to the principal components: 100 * (1 / number_of_individuals)*(ind.coord^2 /

comp_sdev^2). Note that the sum of all the contributions per column is 100

# Coordinates of individuals
#::::::::::::::::::::::::::::::::::
ind.coord <- res.pca$x
head(ind.coord[, 1:4])

## PC1 PC2 PC3 PC4

## SEBRLE 0.191 -1.554 -0.628 0.0821
## CLAY 0.790 -2.420 1.357 1.2698
## BERNARD -1.329 -1.612 -0.196 -1.9209
## YURKOV -0.869 0.433 -2.474 0.6972
## ZSIVOCZKY -0.106 2.023 1.305 -0.0993
## McMULLEN 0.119 0.992 0.844 1.3122

# Cos2 of individuals
#:::::::::::::::::::::::::::::::::
# 1. square of the distance between an individual and the
# PCA center of gravity
center <- res.pca$center
scale<- res.pca$scale
getdistance <- function(ind_row, center, scale){
return(sum(((ind_row-center)/scale)^2))
}
d2 <- apply(decathlon2.active,1,getdistance, center, scale)
# 2. Compute the cos2. The sum of each row is 1
cos2 <- function(ind.coord, d2){return(ind.coord^2/d2)}
ind.cos2 <- apply(ind.coord, 2, cos2, d2)
head(ind.cos2[, 1:4])

## PC1 PC2 PC3 PC4

## SEBRLE 0.00753 0.4975 0.08133 0.00139
## CLAY 0.04870 0.4570 0.14363 0.12579
## BERNARD 0.19720 0.2900 0.00429 0.41182
## YURKOV 0.09611 0.0238 0.77823 0.06181
## ZSIVOCZKY 0.00157 0.5764 0.23975 0.00139
## McMULLEN 0.00218 0.1522 0.11014 0.26649

# Contributions of individuals
#:::::::::::::::::::::::::::::::
contrib <- function(ind.coord, comp.sdev, n.ind){
100*(1/n.ind)*ind.coord^2/comp.sdev^2

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}
ind.contrib <- t(apply(ind.coord, 1, contrib,
res.pca$sdev, nrow(ind.coord)))
head(ind.contrib[, 1:4])

## PC1 PC2 PC3 PC4

## SEBRLE 0.0385 5.712 1.385 0.0357
## CLAY 0.6581 13.854 6.460 8.5557
## BERNARD 1.8627 6.144 0.135 19.5783
## YURKOV 0.7969 0.443 21.476 2.5794
## ZSIVOCZKY 0.0118 9.682 5.975 0.0523
## McMULLEN 0.0148 2.325 2.497 9.1353

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0 You are not authorized to post a comment

Alam 11/11/2018 at 12h13 #642

Visitor
Thank you very much for this nice tutorial.

I have one problem. How to italize the variable name in PCA correlation circle plot.

I am looking forward to hearing.

Mike 10/18/2018 at 09h57 #633

Visitor
Sorry to Necro this thread, but I have to say, what a fantastic guide! It has come in very
helpful. Thank you so much for putting this together. I'm curious if anyone else has
had trouble plotting the ellipses?

When I try to run the code under the "Qualitative / categorical variables" section I am
returned with this error:

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<Computation failed in `stat_conf_ellipse()`: missing value where TRUE/FALSE

needed>

I looked up Stat_conf_ellipse to learn more about it, loaded ggpubr, and added it to my
command. After running it, the plot appears with the correct groupings but no ellipses,
along with the following error:
<Error in .check_axes(axes, .length = 2) : axes should be of length 2>

My plot scale is 2 so this makes sense, the length of the axes needs to fit in the plot, so
less than 2. I change this and retry, and then I get <Error in check_axes(axes, .length =
0.5) : could not find function "check_axes",>.

I have tried numerous combinations using "stat_conf_ellipse" and none of them have
worked. I nested it in the fviz_pca_ind command, added it on the end with a +, add and
remove functions from the stat_conf_ellipse help page.....nothing I try is working.

Does anyone have experience with this and thoughts on why it might be failing? Again,
it plots fine with proper groups and colors, but no ellipses. Here was the last iteration
of code I had:

fviz_pca_ind(mydata.pca, col.ind = groups, palette = c("#00AFBB", "#FC4E07",

"#bb00a8"),addEllipses = TRUE, ellipse.type = "confidence",legend.title = "Groups",re-
pel = TRUE, stat_conf_ellipse(position = "identity", na.rm = FALSE, show.legend = NA, in-
herit.aes = true, level = 0.95, npoint = 100, bary = true))

The error on the above code: Error in .check_axes(axes, .length = 2) : axes should be of
length 2

Thanks for any help!

Konig 11/19/2017 at 17h46 #303

Visitor
Hi there,
Email 1
Could you help me out interpreting the correlation of Rank and Points against the PCs?
Is there a way to determine whether these are statistically significant to the PCA re-
sults? Thanks!

Visitor 11/07/2017 at 19h13 #289

Visitor
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