eigenvalue: Extract and visualize the eigenvalues/variances of dimensions

In factoextra: Extract and Visualize the Results of Multivariate Data Analyses

Description

Eigenvalues correspond to the amount of the variation explained by each principal component (PC).

• get_eig(): Extract the eigenvalues/variances of the principal dimensions

• fviz_eig(): Plot the eigenvalues/variances against the number of dimensions

• get_eigenvalue(): an alias of get_eig()

• fviz_screeplot(): an alias of fviz_eig()

These functions support the results of Principal Component Analysis (PCA), Correspondence Analysis (CA), Multiple Correspondence Analysis (MCA), Factor Analysis of Mixed Data (FAMD), Multiple Factor Analysis (MFA) and Hierarchical Multiple Factor Analysis (HMFA) functions.

Usage

get_eig(X)

get_eigenvalue(X)

fviz_eig(
  X,
  choice = c("variance", "eigenvalue"),
  geom = c("bar", "line"),
  barfill = "steelblue",
  barcolor = "steelblue",
  linecolor = "black",
  ncp = 10,
  addlabels = FALSE,
  hjust = 0,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  ggtheme = theme_minimal(),
  ...
)

fviz_screeplot(...)

Arguments

X	an object of class PCA, CA, MCA, FAMD, MFA and HMFA [FactoMineR]; prcomp and princomp [stats]; dudi, pca, coa and acm [ade4]; ca and mjca [ca package].
choice	a text specifying the data to be plotted. Allowed values are "variance" or "eigenvalue".
geom	a text specifying the geometry to be used for the graph. Allowed values are "bar" for barplot, "line" for lineplot or c("bar", "line") to use both types.
barfill	fill color for bar plot.
barcolor	outline color for bar plot.
linecolor	color for line plot (when geom contains "line").
ncp	a numeric value specifying the number of dimensions to be shown.
addlabels	logical value. If TRUE, labels are added at the top of bars or points showing the information retained by each dimension.
hjust	horizontal adjustment of the labels.
main, xlab, ylab	plot main and axis titles.
ggtheme	function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....
...	optional arguments to be passed to the function ggpar.

Value

• get_eig() (or get_eigenvalue()): returns a data.frame containing 3 columns: the eigenvalues, the percentage of variance and the cumulative percentage of variance retained by each dimension.

• fviz_eig() (or fviz_screeplot()): returns a ggplot2

Author(s)

Alboukadel Kassambara [e-mail]

References

http://www.sthda.com/english/

See Also

fviz_pca, fviz_ca, fviz_mca, fviz_mfa, fviz_hmfa

Examples

# Principal Component Analysis
# ++++++++++++++++++++++++++
data(iris)
res.pca <- prcomp(iris[, -5],  scale = TRUE)

# Extract eigenvalues/variances
get_eig(res.pca)

# Default plot
fviz_eig(res.pca, addlabels = TRUE, ylim = c(0, 85))
  
# Scree plot - Eigenvalues
fviz_eig(res.pca, choice = "eigenvalue", addlabels=TRUE)

# Use only bar  or line plot: geom = "bar" or geom = "line"
fviz_eig(res.pca, geom="line")
 
## Not run:          
# Correspondence Analysis
# +++++++++++++++++++++++++++++++++
library(FactoMineR)
data(housetasks)
res.ca <- CA(housetasks, graph = FALSE)
get_eig(res.ca)
fviz_eig(res.ca, linecolor = "#FC4E07",
   barcolor = "#00AFBB", barfill = "#00AFBB")

# Multiple Correspondence Analysis
# +++++++++++++++++++++++++++++++++
library(FactoMineR)
data(poison)
res.mca <- MCA(poison, quanti.sup = 1:2, 
              quali.sup = 3:4, graph=FALSE)
get_eig(res.mca)
fviz_eig(res.mca, linecolor = "#FC4E07",
   barcolor = "#2E9FDF", barfill = "#2E9FDF")

## End(Not run)

factoextra documentation built on April 2, 2020, 1:09 a.m.