PCAA - Principal Component Analysis

2017/4/9 ade4 and factoextra : Principal Component Analysis R software and data mining Easy Guides Wiki STHDA
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Principal Component Analysis ‐ R software and data mining
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 ade4 and factoextra : Principal Component Analysis ‐ R software and data mining
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Tools
Required packages
Prepare the data
Principal component analysis
Variances of the principal components
Extract the eigenvalues
Make a scree plot using ade4 base graphics
Make the scree plot using the package factoextra
Graph of variables : the circle of correlations
Coordinates of variables on the principal components
Graph of variables using ade4 base graph
Graph of variables using factoextra
Cos2 : quality of the representation for variables on the factor map
Contributions of the variables to the principal components
Graph of individuals
Coordinates of individuals on the principal components
Cos2 : quality of the representation for individuals on the principal components
Contribution of the individuals to the princial components
Graph of individuals using ade4 base graph
Biplot of individuals and variables using ade4
Graph of individuals using factoextra
Change the color of individuals by groups
Principal component analysis using supplementary individuals and variables
Supplementary individuals
Supplementary quantitative variables
Infos
http://www.sthda.com/english/wiki/ade4andfactoextraprincipalcomponentanalysisrsoftwareanddatamining 1/42
This R tutorial describes how to perform a Principal Component Analysis (PCA) using R software and ade4
package.
Required packages
The package ade4 can be installed and loaded as follow :
install.packages("ade4")
library("ade4")
The package factoextra is used for the visualization of the principal component analysis results
factoextra can be installed as follow :
# install.packages("devtools")
devtools::install_github("kassambara/factoextra")
Load it :
library("factoextra")
Prepare the data
We’ll used the data sets decathlon2 from the package factoextra :
data(decathlon2)
head(decathlon2[, 1:6])
X100m Long.jump Shot.put High.jump X400m X110m.hurdle

SEBRLE 11.04 7.58 14.83 2.07 49.81 14.69
CLAY 10.76 7.40 14.26 1.86 49.37 14.05
BERNARD 11.02 7.23 14.25 1.92 48.93 14.99
YURKOV 11.34 7.09 15.19 2.10 50.42 15.31
ZSIVOCZKY 11.13 7.30 13.48 2.01 48.62 14.17
McMULLEN 10.83 7.31 13.76 2.13 49.91 14.38
 This data is a subset of decathlon data in FactoMineR package

As illustrated below, the data used here describes athletes’ performance during two sporting events (Desctar and
OlympicG). It contains 27 individuals (athletes) described by 13 variables :
 Only some of these individuals and variables will be used to perform the principal component analysis
(PCA).
The coordinates of the remaining individuals and variables on the factor map will be predicted after the
PCA.
In PCA terminology, our data contains :
Active individuals (in blue, rows 1:23) : Individuals that are used during the principal component
analysis.
Supplementary individuals (in green, rows 24:27) : The coordinates of these individuals will be predicted
using the PCA informations and parameters obtained with active individuals/variables
Active variables (in pink, columns 1:10) : Variables that are used for the principal component analysis.
Supplementary variables : As supplementary individuals, the coordinates of these variables will be
predicted also.
Supplementary continuous variables : Columns 11 and 12 corresponding respectively to the rank and the
points of athletes.
Supplementary qualitative variables : Column 13 corresponding to the two athletic meetings (2004
Olympic Game or 2004 Decastar). This factor variables will be used to color individuals by groups.
Extract only active individuals and variables for principal component analysis:
decathlon2.active <- decathlon2[1:23, 1:10]

head(decathlon2.active[, 1:6])

SEBRLE 11.04 7.58 14.83 2.07 49.81 14.69
CLAY 10.76 7.40 14.26 1.86 49.37 14.05

BERNARD 11.02 7.23 14.25 1.92 48.93 14.99
YURKOV 11.34 7.09 15.19 2.10 50.42 15.31
ZSIVOCZKY 11.13 7.30 13.48 2.01 48.62 14.17
McMULLEN 10.83 7.31 13.76 2.13 49.91 14.38
Principal component analysis

The function dudi.pca() [in ade4 package] can be used. A simplified format is :
dudi.pca(df, center = TRUE, scale = TRUE,

scannf = TRUE, nf = 2)
df : a data frame. Rows are individuals and columns are numeric variables
center : a logical value specifying whether the variables should be shifted to be zero centered.
scale : a logical value. If TRUE, the data are scaled to unit variance before the analysis. This
standardization to the same scale avoids some variables to become dominant just because of their large
measurement units.
scannf : a logical value specifying whether the scree plot should be displayed
nf : number of dimensions kept in the final results.
In the R code below, the PCA is performed only on the active individuals/variables :
library("ade4")
res.pca <- dudi.pca(decathlon2.active, scannf = FALSE, nf = 5)
Variances of the principal components
Extract the eigenvalues
Eigenvalues measure the amount of variation retained by a principal component :
summary(res.pca)
Class: pca dudi

Call: dudi.pca(df = decathlon2.active, scannf = FALSE, nf = 5)
Total inertia: 10
Eigenvalues:
Ax1 Ax2 Ax3 Ax4 Ax5
4.1242 1.8385 1.2391 0.8194 0.7016
Projected inertia (%):
Ax1 Ax2 Ax3 Ax4 Ax5
41.242 18.385 12.391 8.194 7.016
Cumulative projected inertia (%):
Ax1 Ax1:2 Ax1:3 Ax1:4 Ax1:5

41.24 59.63 72.02 80.21 87.23
(Only 5 dimensions (out of 10) are shown)
You can also use the package factoextra to extract the eigenvalues :
eig.val <- get_eigenvalue(res.pca)
head(eig.val)
eigenvalue variance.percent cumulative.variance.percent

Dim 1 4.1242133 41.242133 41.24213
Dim 2 1.8385309 18.385309 59.62744
Dim 3 1.2391403 12.391403 72.01885
Dim 4 0.8194402 8.194402 80.21325
Dim 5 0.7015528 7.015528 87.22878
Dim 6 0.4228828 4.228828 91.45760
Make a scree plot using ade4 base graphics
The function scree plot() can be used to represent the amount of inertia (variance) associated with each principal
component (PC).
A simplified format is :
screeplot(x, ncps = length(x$eig), type = c("barplot", "lines"))
x : an object of class dudi

ncps : the number of components to be plotted
type : the type of plot
Example of usage :
screeplot(res.pca, main ="Screeplot - Eigenvalues")
You can also customize the plot using the standard barplot() function. In the R code below, we’ll draw the
percentage of variances retained by each component :
barplot(eig.val[, 2], names.arg=1:nrow(eig.val),

main = "Variances",
xlab = "Principal Components",
ylab = "Percentage of variances",
col ="steelblue")
# Add connected line segments to the plot
lines(x = 1:nrow(eig.val), eig.val[, 2],
type="b", pch=19, col = "red")
 ~60% of the information (variances) contained in the data are retained by the first two principal
components.
Make the scree plot using the package factoextra
fviz_screeplot(res.pca, ncp=10)
Graph of variables : the circle of correlations
Coordinates of variables on the principal components
The coordinates of the variables on the factor map are :
# Column coordinates
head(res.pca$co)
Comp1 Comp2 Comp3 Comp4 Comp5

X100m 0.8506257 -0.17939806 -0.3015564 0.03357320 0.1944440
Long.jump -0.7941806 0.28085695 0.1905465 -0.11538956 -0.2331567
Shot.put -0.7339127 0.08540412 -0.5175978 0.12846837 0.2488129
High.jump -0.6100840 -0.46521415 -0.3300852 0.14455012 -0.4027002
X400m 0.7016034 0.29017826 -0.2835329 0.43082552 -0.1039085
X110m.hurdle 0.7641252 -0.02474081 -0.4488873 -0.01689589 -0.2242200
Graph of variables using ade4 base graph
The function s.corcircle() can be used to plot the correlation circle. A simplified format is :
s.corcircle(dfxy, label = row.names(dfxy), grid = TRUE,

box = FALSE)
dfxy : a data frame specifying the coordinates of variables

label : a vector of strings specifying point labels
grid : a logical value specifying whether a grid in the background of the plot should be drawn
box : a logical value indicating whether a box should be drawn
# Graph of variables
s.corcircle(res.pca$co)
Graph of variables using factoextra
The function fviz_pca_var() is used to visualize variables :
# Default plot
fviz_pca_var(res.pca)
# Change color and theme

fviz_pca_var(res.pca, col.var="steelblue")+
theme_minimal()
Read more about the function fviz_pca_var() : Graph of variables ‐ Principal Component Analysis
 How to calculate the cos2 and the contribution of variables?
The cos2 and the contributions of variables (columns) / individuals (rows) are calculated using the function
inertia.dudi() as follow :
inertia <- inertia.dudi(res.pca, row.inertia = TRUE,

col.inertia = TRUE)
 Note that, the contributions and the cos2 are printed in 1/10 000. The sign is the sign of the coordinates.
Cos2 : quality of the representation for variables on the factor map
The squared coordinates of variables are called cos2.

A high cos2 indicates a good representation of the variable on the principal component. In this case the
variable is positioned close to the circumference of the correlation circle.
A low cos2 indicates that the variable is not perfectly represented by the PCs. In this case the variable is
close to the center of the circle.
The cos2 of the variables are :
# relative contributions of columns

var.cos2 <- abs(inertia$col.rel/10000)
head(var.cos2)
Comp1 Comp2 Comp3 Comp4 Comp5 con.tra

X100m 0.7236 0.0322 0.0909 0.0011 0.0378 0.1
Long.jump 0.6307 0.0789 0.0363 0.0133 0.0544 0.1
Shot.put 0.5386 0.0073 0.2679 0.0165 0.0619 0.1
High.jump 0.3722 0.2164 0.1090 0.0209 0.1622 0.1
X400m 0.4922 0.0842 0.0804 0.1856 0.0108 0.1
X110m.hurdle 0.5839 0.0006 0.2015 0.0003 0.0503 0.1
It can also be calculated as follow :
# squared coordinates
head(res.pca$co^2)

X100m 0.7235641 0.0321836641 0.09093628 0.0011271597 0.03780845
Long.jump 0.6307229 0.0788806285 0.03630798 0.0133147506 0.05436203
Shot.put 0.5386279 0.0072938636 0.26790749 0.0165041211 0.06190783
High.jump 0.3722025 0.2164242070 0.10895622 0.0208947375 0.16216747
X400m 0.4922473 0.0842034209 0.08039091 0.1856106269 0.01079698
X110m.hurdle 0.5838873 0.0006121077 0.20149984 0.0002854712 0.05027463
 Using factoextra package, the color of variables can be automatically controlled by the value of their
cos2.
fviz_pca_var(res.pca, col.var="contrib")+
scale_color_gradient2(low="white", mid="blue",
high="red", midpoint=55) + theme_minimal()
Contributions of the variables to the principal components
The contributions can be printed in % as follow :
# absolute contribution of columns

var.contrib <- inertia$col.abs/100
head(var.contrib)

X100m 17.54 1.75 7.34 0.14 5.39
Long.jump 15.29 4.29 2.93 1.62 7.75
Shot.put 13.06 0.40 21.62 2.01 8.82
High.jump 9.02 11.77 8.79 2.55 23.12
X400m 11.94 4.58 6.49 22.65 1.54
X110m.hurdle 14.16 0.03 16.26 0.03 7.17
 Note that, You can also use the function get_pca_var() [from factoextra package]. It provides a list of
matrices containing all the results for the active variables (coordinates, correlation between variables and
axes, squared cosine and contributions).
var <- get_pca_var(res.pca)

names(var)
[1] "coord" "cor" "cos2" "contrib"
# Contributions of variables
head(var$contrib)
Dim.1 Dim.2 Dim.3 Dim.4 Dim.5

X100m 17.544293 1.7505098 7.338659 0.13755240 5.389252
Long.jump 15.293168 4.2904162 2.930094 1.62485936 7.748815
Shot.put 13.060137 0.3967224 21.620432 2.01407269 8.824401
High.jump 9.024811 11.7715838 8.792888 2.54987951 23.115504
X400m 11.935544 4.5799296 6.487636 22.65090599 1.539012
X110m.hurdle 14.157544 0.0332933 16.261261 0.03483735 7.166193
 Using factoextra package, the color of variables can be automatically controlled by the value of their
contributions
fviz_pca_var(res.pca, col.var="contrib") +
high="red", midpoint=50) + theme_minimal()
 This is helpful to highlight the most important variables for the principal components.
The most important variables for a given PC can be visualized using the function fviz_pca_contrib()[factoextra
package] :
(factoextra >= 1.0.1 is required)
# Contributions of variables on PC1

fviz_pca_contrib(res.pca, choice = "var", axes = 1)

fviz_pca_contrib(res.pca, choice = "var", axes = 2)
Read more about fviz_pca_contrib() : Principal Component Analysis: How to reveal the most important variables
in your data?
Graph of individuals
Coordinates of individuals on the principal components
The coordinates of the individuals on the factor maps can be extracted as follow :
# The row coordinates

head(res.pca$li)
Axis1 Axis2 Axis3 Axis4 Axis5

SEBRLE -0.1955047 1.5890567 -0.6424912 0.08389652 -1.16829387
CLAY -0.8078795 2.4748137 1.3873827 1.29838232 0.82498206
BERNARD 1.3591340 1.6480950 -0.2005584 -1.96409420 -0.08419345
YURKOV 0.8889532 -0.4426067 -2.5295843 0.71290837 -0.40782264
ZSIVOCZKY 0.1081216 -2.0688377 1.3342591 -0.10152796 0.20145217
McMULLEN -0.1212195 -1.0139102 0.8625170 1.34164291 -1.62151286
Cos2 : quality of the representation for individuals on the principal components
# relative contributions of rows

ind.cos2 <- abs(inertia$row.rel)/10000
head(ind.cos2)
Axis1 Axis2 Axis3 Axis4 Axis5 con.tra

SEBRLE 0.0075 0.4975 0.0813 0.0014 0.2689 0.0221
CLAY 0.0487 0.4570 0.1436 0.1258 0.0508 0.0583
BERNARD 0.1972 0.2900 0.0043 0.4118 0.0008 0.0407
YURKOV 0.0961 0.0238 0.7782 0.0618 0.0202 0.0357
ZSIVOCZKY 0.0016 0.5764 0.2398 0.0014 0.0055 0.0323
McMULLEN 0.0022 0.1522 0.1101 0.2665 0.3893 0.0294
Contribution of the individuals to the princial components
The contributions can be printed in % as follow :
# absolute contributions of rows

ind.contrib <- inertia$row.abs/100
head(ind.contrib)

SEBRLE 0.04 5.97 1.45 0.04 8.46
CLAY 0.69 14.48 6.75 8.94 4.22
BERNARD 1.95 6.42 0.14 20.47 0.04
YURKOV 0.83 0.46 22.45 2.70 1.03
ZSIVOCZKY 0.01 10.12 6.25 0.05 0.25
McMULLEN 0.02 2.43 2.61 9.55 16.29
 It’s also possible to use the function get_pca_ind() [from factoextra package]. factoextra provides, a list
of matrices containing all the results for the active individuals (coordinates, squared cosine and
contributions)./span>
ind <- get_pca_ind(res.pca)

names(ind)
[1] "coord" "cos2" "contrib"
# Contributions of individuals
head(ind$contrib)
Dim.1 Dim.2 Dim.3 Dim.4 Dim.5

SEBRLE 0.04029447 5.9714533 1.4483919 0.03734589 8.45894063
CLAY 0.68805664 14.4839248 6.7537381 8.94458283 4.21794385
BERNARD 1.94740183 6.4234107 0.1411345 20.46819433 0.04393073
YURKOV 0.83308415 0.4632733 22.4517396 2.69663605 1.03075263
ZSIVOCZKY 0.01232413 10.1217143 6.2464325 0.05469230 0.25151025
McMULLEN 0.01549089 2.4310854 2.6102794 9.55055888 16.29493304
Use the function fviz_pca_contrib()[factoextra package] to visualize the most contributing individuals :
(factoextra >= 1.0.1 is required)

fviz_pca_contrib(res.pca, choice = "ind", axes = 1)

fviz_pca_contrib(res.pca, choice = "ind", axes = 2)
Read more about fviz_pca_contrib() : Principal Component Analysis: How to reveal the most important variables
in your data?
Graph of individuals using ade4 base graph
The function s.label() can be used. A simplified format is :
s.label(dfxy, xax = 1, yax = 2)
dfxy : a data frame with at least two coordinates

xax : a numeric value specifying the column number containing x values
yax : a numeric value specifying the column number containing y values
Factor map of individuals :
s.label(res.pca$li, xax = 1, yax = 2)
Biplot of individuals and variables using ade4
Biplot can be drawn using the combination of the two functions below :
s.label() to plot individuals
s.arrow() to add variables
# Plot of individuals
s.label(res.pca$li, xax = 1, yax = 2)
# Add variables
s.arrow(7*res.pca$c1, add.plot = TRUE)
It’s also possible to use the function scatter() or biplot() :
scatter(res.pca)
# Remove the scree plot (posieig ="none")

# Remove row labels (clab.row = 0)
scatter(res.pca, posieig = "none", clab.row = 0)
NULL
 Note that, to remove variable labels the argument clab.col = 0 can be used.
Graph of individuals using factoextra
The function fviz_pca_ind() is used to visualize individuals :
fviz_pca_ind(res.pca)
Control automatically the color of individuals using the cos2 values (the quality of the individuals on the factor
map) :
fviz_pca_ind(res.pca, col.ind="cos2") +
high="red", midpoint=0.50)
Change the theme :
fviz_pca_ind(res.pca, col.ind="cos2") +
high="red", midpoint=0.50) + theme_minimal()
Read more about fviz_pca_ind() : Graph of individuals ‐ principal component analysis

Make a biplot of individuals and variables :
fviz_pca_biplot(res.pca, geom = "text") +

theme_minimal()
Read more about fviz_pca_biplot() : Biplot of individuals and variables ‐ principal component analysis
Change the color of individuals by groups
The data sets decathlon2 contain a supplementary qualitative variable at columns 13 corresponding to the type
of competitions.
Qualitative variable can be helpful for interpreting the data and for coloring individuals by groups :
# Data for the supplementary qualitative variables

quali.sup <- as.factor(decathlon2[1:23, 13])
head(quali.sup)
[1] Decastar Decastar Decastar Decastar Decastar Decastar

Levels: Decastar OlympicG
The function s.class() can be used to visualize the classes (groups) of points :
s.class(dfxy, fac, xax = 1, yax = 2, col)
dfxy : a data frame containing the two columns for x and y axes
fac : a factor variable partitioning the individuals in classes
xax, yax : a numeric value specifying the column number containing x and y values
col : a vector of colors used to draw each class in a different color
Color individuals by groups :
s.class(res.pca$li, fac = quali.sup, xax = 1, yax = 2)
# Change the colors

s.class(res.pca$li, fac = quali.sup, col = c("blue", "red"))
# Make a biplot
# clab.row : hide the label for rows (individuals)
res <- scatter(res.pca, clab.row = 0, posieig = "none")
s.class(res.pca$li, fac = quali.sup, col = c("blue", "red"),
add.plot = TRUE)
# Customize the biplot

# - remove row labels (clab.row = 0)
# - hide the scree plot (posieig = 0)
# - remove stars (cstar = 0)
# - remove ellipse (cellipse = 0)
add.plot = TRUE, cstar = 0, cellipse = 0)
# remove labels for classes (clabel = 0)

add.plot = TRUE, cstar = 0, cellipse = 0, clabel = 0)
It’s also possible to use factoextra :
fviz_pca_ind(res.pca, habillage = quali.sup,

addEllipses =TRUE, ellipse.level = 0.68) +
theme_minimal()
Elegant biplot using factoextra and iris data :
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
# The variable Species (index = 5) is removed

# before PCA analysis
iris.pca <- dudi.pca(iris[,-5], scannf = FALSE, nf = 2)
Now, let’s :
make a biplot of individuals and variables
change the color of individuals by groups
change the transparency of variable colors by their contribution values
show only the labels for variables
fviz_pca_biplot(iris.pca,
habillage = iris$Species, addEllipses = TRUE,
col.var = "red", alpha.var ="cos2",
label = "var") +
scale_color_brewer(palette="Dark2")+
theme_minimal()
Principal component analysis using supplementary individuals and variables
 Ascolumns
described above, the data sets decathlon2 contain supplementary continuous variables (quanti.sup,
11:12), supplementary qualitative variables (quali.sup, column 13) and supplementary
individuals (ind.sup, rows 24:27)
Supplementary variables / individuals are not used to compute the principal component. Their coordinates are
predicted using only the information provided by the performed principal component analysis on active variables /
individuals.
The functions suprow() and supcol() [in ade4 package] are used to calculate the coordinates of supplementary
rows (individuals) and columns (variables), respectively.
The simplified formats are :
# For supplementary individuals (rows)

suprow(x, Xsup)
# For supplementary variables (columns)
supcol(x, Xsup)
Supplementary individuals
# Data for the supplementary individuals

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

KARPOV 11.02 7.30 14.77 2.04 48.37 14.09
WARNERS 11.11 7.60 14.31 1.98 48.68 14.23
Nool 10.80 7.53 14.26 1.88 48.81 14.80
Drews 10.87 7.38 13.07 1.88 48.51 14.01
Predict the coordinates of the supplementary individuals :
ind.sup.pca <- suprow(res.pca, ind.sup)

names(ind.sup.pca)
[1] "tabsup" "lisup"
# coordinates
ind.sup.coord <- ind.sup.pca$lisup
head(ind.sup.coord)

KARPOV -0.7947206 0.77951227 1.6330203 1.7242283 0.75070396
WARNERS 0.3864645 -0.12159237 1.7387332 -0.7063341 0.03230011
Nool 0.5591306 1.97748871 0.4830358 -2.2784526 0.25461493
Drews 1.1092038 0.01741477 3.0488182 -1.5343468 0.32642192
 How to visualize supplementary individuals on the factor map?
The function fviz_add() is used :
# Plot of active individuals

p <- fviz_pca_ind(res.pca)
# Add supplementary individuals
fviz_add(p, ind.sup.coord, color ="blue")
 How to calculate the cos2 (quality of the representation) for supplementary individuals?
cos2.func <-function(x){x^2/sum(x^2)}
ind.sup.cos2 <- t(apply(ind.sup.coord, 1, cos2.func))
head(ind.sup.cos2)

KARPOV 0.08486144 8.164458e-02 0.35831467 0.3994579 0.0757214366
WARNERS 0.04050537 4.009646e-03 0.81989704 0.1353050 0.0002829447
Nool 0.03218782 4.026179e-01 0.02402281 0.5344967 0.0066747159
Drews 0.09473792 2.335268e-05 0.71575477 0.1812793 0.0082046453
Supplementary quantitative variables
# Data for the supplementary quantitative variables

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
 Remember that, rows 24:27 are supplementary individuals. We don’t want them in this current analysis.
This is why, I extracted only rows 1:23.
Predict the coordinates of the supplementary variables :

(You have to scale the supplementary variables before the analysis as the PCA has been performed on scaled
data.)
quanti.pca <- supcol(res.pca, scale(quanti.sup))

names(quanti.pca)
[1] "tabsup" "cosup"
# coordinates
quanti.coord <- quanti.pca$cosup
head(quanti.coord)

Rank 0.6860587 -0.2398049 0.1793975 0.0545264 0.07220371
Points -0.9425246 0.0759751 -0.1545490 -0.1625770 0.03046248
Visualize supplementary variables on the factor map using factoextra :
# Plot of active variables

p <- fviz_pca_var(res.pca)
# Add supplementary active variables
fviz_add(p, quanti.coord, geom="arrow", color ="blue")
# Get the cos2 of the supplementary quantitative variables

(quanti.coord^2)[, 1:4]
Comp1 Comp2 Comp3 Comp4

Rank 0.4706766 0.057506383 0.03218347 0.002973128
Points 0.8883526 0.005772216 0.02388540 0.026431296
Infos
 This analysis has been performed using R software (ver. 3.1.2) and ggplot2 (ver. 1.0.0)
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PCAA - Principal Component Analysis

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2017/4/9 ade4 and factoextra : Principal Component Analysis ­ R software and data mining ­ Easy Guides ­ Wiki ­ STHDA

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Prepare the data

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

 This data is a subset of decathlon data in FactoMineR package

In PCA terminology, our data contains :

decathlon2.active <- decathlon2[1:23, 1:10]

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

CLAY 10.76 7.40 14.26 1.86 49.37 14.05

Principal component analysis

dudi.pca(df, center = TRUE, scale = TRUE,

Variances of the principal components

Extract the eigenvalues

Eigenvalues measure the amount of variation retained by a principal component :

Class: pca dudi

Ax1 Ax1:2 Ax1:3 Ax1:4 Ax1:5

eigenvalue variance.percent cumulative.variance.percent

Make a scree plot using ade4 base graphics

screeplot(x, ncps = length(x$eig), type = c("barplot", "lines"))

x : an object of class dudi

screeplot(res.pca, main ="Screeplot - Eigenvalues")

barplot(eig.val[, 2], names.arg=1:nrow(eig.val),

Make the scree plot using the package factoextra

Graph of variables : the circle of correlations

Coordinates of variables on the principal components

The coordinates of the variables on the factor map are :

Comp1 Comp2 Comp3 Comp4 Comp5

Graph of variables using ade4 base graph

s.corcircle(dfxy, label = row.names(dfxy), grid = TRUE,

dfxy : a data frame specifying the coordinates of variables

Graph of variables using factoextra

The function fviz_pca_var() is used to visualize variables :

# Change color and theme

 How to calculate the cos2 and the contribution of variables?

inertia <- inertia.dudi(res.pca, row.inertia = TRUE,

Cos2 : quality of the representation for variables on the factor map

The squared coordinates of variables are called cos2.

# relative contributions of columns

Comp1 Comp2 Comp3 Comp4 Comp5 con.tra

It can also be calculated as follow :

Comp1 Comp2 Comp3 Comp4 Comp5

Contributions of the variables to the principal components

The contributions can be printed in % as follow :

# absolute contribution of columns

Comp1 Comp2 Comp3 Comp4 Comp5

var <- get_pca_var(res.pca)

[1] "coord" "cor" "cos2" "contrib"

Dim.1 Dim.2 Dim.3 Dim.4 Dim.5

# Contributions of variables on PC1

# Contributions of variables on PC2

Coordinates of individuals on the principal components

# The row coordinates

Axis1 Axis2 Axis3 Axis4 Axis5

Cos2 : quality of the representation for individuals on the principal components

# relative contributions of rows

Axis1 Axis2 Axis3 Axis4 Axis5 con.tra

Contribution of the individuals to the princial components

The contributions can be printed in % as follow :

# absolute contributions of rows

Axis1 Axis2 Axis3 Axis4 Axis5

ind <- get_pca_ind(res.pca)

[1] "coord" "cos2" "contrib"

2017/4/9 ade4 and factoextra : Principal Component Analysis R software and data mining Easy Guides Wiki STHDA