- Description
- Install and load factoextra
- Usage
- Arguments
- Value
- Examples
- Principal component analysis
- fviz_pca_ind(): Graph of individuals
- fviz_pca_var(): Graph of variables
- fviz_pca_biplot(): Biplot of individuals of variables
- Infos
Draw the graph of individuals/variables from the output of Principal Component Analysis (PCA).
The following functions, from factoextra package are use:
- fviz_pca_ind(): Graph of individuals
- fviz_pca_var(): Graph of variables
- fviz_pca_biplot() (or fviz_pca()): Biplot of individuals and variables
The package devtools is required for the installation as factoextra is hosted on github.
# install.packages("devtools")library("devtools")install_github("kassambara/factoextra")Load factoextra :
library("factoextra")# Graph of individualsfviz_pca_ind(X, axes = c(1, 2), geom = c("point", "text"), label = "all", invisible = "none", labelsize = 4, pointsize = 2, habillage = "none", addEllipses = FALSE, ellipse.level = 0.95, col.ind = "black", col.ind.sup = "blue", alpha.ind = 1, select.ind = list(name = NULL, cos2 = NULL, contrib = NULL), jitter = list(what = "label", width = NULL, height = NULL), ...)# Graph of variablesfviz_pca_var(X, axes = c(1, 2), geom = c("arrow", "text"), label = "all", invisible = "none", labelsize = 4, col.var = "black", alpha.var = 1, col.quanti.sup = "blue", col.circle = "grey70", select.var = list(name =NULL, cos2 = NULL, contrib = NULL), jitter = list(what = "label", width = NULL, height = NULL))# Biplot of individuals and variablesfviz_pca_biplot(X, axes = c(1, 2), geom = c("point", "text"), label = "all", invisible = "none", labelsize = 4, pointsize = 2, habillage = "none", addEllipses = FALSE, ellipse.level = 0.95, col.ind = "black", col.ind.sup = "blue", alpha.ind = 1, col.var = "steelblue", alpha.var = 1, col.quanti.sup = "blue", col.circle = "grey70", select.var = list(name = NULL, cos2 = NULL, contrib= NULL), select.ind = list(name = NULL, cos2 = NULL, contrib = NULL), jitter = list(what = "label", width = NULL, height = NULL), ...)# An alias of fviz_pca_biplot()fviz_pca(X, ...)| Argument | Description |
|---|---|
| X | an object of class PCA [FactoMineR]; prcomp and princomp [stats]; dudi and pca [ade4]. |
| axes | a numeric vector of length 2 specifying the dimensions to be plotted. |
| geom | a text specifying the geometry to be used for the graph. Allowed values are the combination of c(“point”, “arrow”, “text”). Use “point” (to show only points); “text” to show only labels; c(“point”, “text”) or c(“arrow”, “text”) to show both types. |
| label | a text specifying the elements to be labelled. Default value is “all”. Allowed values are “none” or the combination of c(“ind”, “ind.sup”, “quali”, “var”, “quanti.sup”). “ind” can be used to label only active individuals. “ind.sup” is for supplementary individuals. “quali” is for supplementary qualitative variables. “var” is for active variables. “quanti.sup” is for quantitative supplementary variables. |
| invisible | a text specifying the elements to be hidden on the plot. Default value is “none”. Allowed values are the combination of c(“ind”, “ind.sup”, “quali”, “var”, “quanti.sup”). |
| labelsize | font size for the labels. |
| pointsize | the size of points. |
| habillage | an optional factor variable for coloring the observations by groups. Default value is “none”. If X is a PCA object from FactoMineR package, habillage can also specify the supplementary qualitative variable (by its index or name) to be used for coloring individuals by groups (see ?PCA in FactoMineR). |
| addEllipses | logical value. If TRUE, draws ellipses around the individuals when habillage != “none”. |
| ellipse.level | the size of the concentration ellipse in normal probability. |
| col.ind,col.var | colors for individuals and variables, respectively. Possible values include also : “cos2”, “contrib”, “coord”, “x” or “y”. In this case, the colors for individuals/variables are automatically controlled by their qualities of representation (“cos2”), contributions (“contrib”), coordinates (x^2 + y^2, “coord”), x values (“x”) or y values (“y”). To use automatic coloring (by cos2, contrib, ….), make sure that habillage =“none”. |
| col.ind.sup | color for supplementary individuals. |
| alpha.ind,alpha.var | controls the transparency of individual and variable colors, respectively. The value can variate from 0 (total transparency) to 1 (no transparency). Default value is 1. Possible values include also : “cos2”, “contrib”, “coord”, “x” or “y”. In this case, the transparency for the individual/variable colors are automatically controlled by their qualities (“cos2”), contributions (“contrib”), coordinates (x^2 + y^2 , “coord”), x values(“x”) or y values(“y”). To use this, make sure that habillage =“none”. |
| select.ind,select.var | a selection of individuals/variables to be drawn. Allowed values are NULL or a list containing the arguments name, cos2 or contrib:
|
| jitter | a parameter used to jitter the points in order to reduce overplotting. It’s a list containing the objects what, width and height (Ex.; jitter = list(what, width, height)). what: the element to be jittered. Possible values are “point” or “p”; “label” or “l”; “both” or “b”. width: degree of jitter in x direction (ex: 0.2). height: degree of jitter in y direction (ex: 0.2). |
| col.quanti.sup | a color for the quantitative supplementary variables. |
| col.circle | a color for the correlation circle. |
| … | Arguments to be passed to the function fviz_pca_biplot(). |
A ggplot2 plot
Principal component analysis
A principal component analysis (PCA) is performed using the built-in R function prcomp() and iris data:
data(iris)head(iris) Sepal.Length Sepal.Width Petal.Length Petal.Width Species1 5.1 3.5 1.4 0.2 setosa2 4.9 3.0 1.4 0.2 setosa3 4.7 3.2 1.3 0.2 setosa4 4.6 3.1 1.5 0.2 setosa5 5.0 3.6 1.4 0.2 setosa6 5.4 3.9 1.7 0.4 setosa# The variable Species (index = 5) is removed# before the PCA analysisres.pca <- prcomp(iris[, -5], scale = TRUE)fviz_pca_ind(): Graph of individuals
# Default plotfviz_pca_ind(res.pca)
# Change title and axis labelsfviz_pca_ind(res.pca) + labs(title ="PCA", x = "PC1", y = "PC2")
# Change axis limits by specifying the min and maxfviz_pca_ind(res.pca) + xlim(-4, 4) + ylim (-4, 4)
See Also
fviz_pca function - RDocumentationDraw Biplot of PCA in R (2 Examples) | biplot() & fviz_pca_biplot()PCA - Principal Component Analysis Essentials - Articlesfviz_pca: Visualize Principal Component Analysis in factoextra: Extract and Visualize the Results of Multivariate Data Analyses# Use text onlyfviz_pca_ind(res.pca, geom="text")
# Use points onlyfviz_pca_ind(res.pca, geom="point")
# Change the size of pointsfviz_pca_ind(res.pca, geom="point", pointsize = 4)
# Change point color and themefviz_pca_ind(res.pca, col.ind = "blue")+ theme_minimal()
# Control automatically the color of individuals# using the cos2 or the contributions# cos2 = the quality of the individuals on the factor mapfviz_pca_ind(res.pca, col.ind="cos2")
# Gradient colorfviz_pca_ind(res.pca, col.ind="cos2") + scale_color_gradient2(low="white", mid="blue", high="red", midpoint=0.6)
# Change the theme and use only pointsfviz_pca_ind(res.pca, col.ind="cos2", geom = "point") + scale_color_gradient2(low="white", mid="blue", high="red", midpoint=0.6)+ theme_minimal()
# Color by the contributionsfviz_pca_ind(res.pca, col.ind="contrib") + scale_color_gradient2(low="white", mid="blue", high="red", midpoint=4)
# Control the transparency of the color by the# contributionsfviz_pca_ind(res.pca, alpha.ind="contrib") + theme_minimal()
# Color individuals by groupsfviz_pca_ind(res.pca, label="none", habillage=iris$Species)
# Add ellipsesp <- fviz_pca_ind(res.pca, label="none", habillage=iris$Species, addEllipses=TRUE, ellipse.level=0.95)print(p)
# Change group colors using RColorBrewer color palettesp + scale_color_brewer(palette="Dark2") + theme_minimal()
p + scale_color_brewer(palette="Paired") + theme_minimal()
p + scale_color_brewer(palette="Set1") + theme_minimal()
# Change color manuallyp + scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))
# Select and visualize individuals with cos2 > 0.96fviz_pca_ind(res.pca, select.ind = list(cos2 = 0.96))
# Select the top 20 according the cos2fviz_pca_ind(res.pca, select.ind = list(cos2 = 20))
# Select the top 20 contributing individualsfviz_pca_ind(res.pca, select.ind = list(contrib = 20))
# Select by namesfviz_pca_ind(res.pca,select.ind = list(name = c("23", "42", "119")))
fviz_pca_var(): Graph of variables
# Default plotfviz_pca_var(res.pca)
# Use points and textfviz_pca_var(res.pca, geom = c("point", "text"))
# Change color and themefviz_pca_var(res.pca, col.var="steelblue")+ theme_minimal()
# Control variable colors using their contributionsfviz_pca_var(res.pca, col.var="contrib")+ scale_color_gradient2(low="white", mid="blue", high="red", midpoint=96) + theme_minimal()
# Control the transparency of variables using their contributionsfviz_pca_var(res.pca, alpha.var="contrib") + theme_minimal()
# Select and visualize variables with cos2 >= 0.96fviz_pca_var(res.pca, select.var = list(cos2 = 0.96))
# Select the top 3 contributing variablesfviz_pca_var(res.pca, select.var = list(contrib = 3))
# Select by namesfviz_pca_var(res.pca, select.var= list(name = c("Sepal.Width", "Petal.Length")))
fviz_pca_biplot(): Biplot of individuals of variables
fviz_pca_biplot(res.pca)
# Keep only the labels for variablesfviz_pca_biplot(res.pca, label ="var")
# Keep only labels for individualsfviz_pca_biplot(res.pca, label ="ind")
# Hide variablesfviz_pca_biplot(res.pca, invisible ="var")
# Hide individualsfviz_pca_biplot(res.pca, invisible ="ind")
# Control automatically the color of individuals using the cos2fviz_pca_biplot(res.pca, label ="var", col.ind="cos2") + theme_minimal()
# Change the color by groups, add ellipsesfviz_pca_biplot(res.pca, label="var", habillage=iris$Species, addEllipses=TRUE, ellipse.level=0.95)
# Select the top 30 contributing individualsfviz_pca_biplot(res.pca, label="var", select.ind = list(contrib = 30))
This analysis has been performed using R software (ver. 3.2.1) and factoextra (ver. 1.0.3)
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