fviz_cluster {factoextra}

Visualize Clustering Results

Description

Provides ggplot2-based elegant visualization of partitioning methods including kmeans [stats package]; pam, clara and fanny [cluster package]; dbscan [fpc package]; Mclust [mclust package]; HCPC [FactoMineR]; hkmeans [factoextra]. Observations are represented by points in the plot, using principal components if ncol(data) > 2. An ellipse is drawn around each cluster.

Usage

fviz_cluster(
  object,
  data = NULL,
  choose.vars = NULL,
  stand = TRUE,
  axes = c(1, 2),
  geom = c("point", "text"),
  repel = FALSE,
  show.clust.cent = TRUE,
  ellipse = TRUE,
  ellipse.type = "convex",
  ellipse.level = 0.95,
  ellipse.alpha = 0.2,
  shape = NULL,
  pointsize = 1.5,
  labelsize = 12,
  main = "Cluster plot",
  xlab = NULL,
  ylab = NULL,
  outlier.color = "black",
  outlier.shape = 19,
  outlier.pointsize = pointsize,
  outlier.labelsize = labelsize,
  ggtheme = theme_grey(),
  ...
)

Arguments

object

an object of class "partition" created by the functions pam(), clara() or fanny() in cluster package; "kmeans" [in stats package]; "dbscan" [in fpc package]; "Mclust" [in mclust]; "hkmeans", "eclust" [in factoextra]. Possible value are also any list object with data and cluster components (e.g.: object = list(data = mydata, cluster = myclust)).

data

the data that has been used for clustering. Required only when object is a class of kmeans or dbscan.

choose.vars

a character vector containing variables to be considered for plotting.

stand

logical value; if TRUE, data is standardized before principal component analysis

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", "text"). Use "point" (to show only points); "text" to show only labels; c("point", "text") to show both types.

repel

a boolean, whether to use ggrepel to avoid overplotting text labels or not.

show.clust.cent

logical; if TRUE, shows cluster centers

ellipse

logical value; if TRUE, draws outline around points of each cluster

ellipse.type

Character specifying frame type. Possible values are 'convex', 'confidence' or types supported by stat_ellipse including one of c("t", "norm", "euclid").

ellipse.level

the size of the concentration ellipse in normal probability. Passed for ggplot2::stat_ellipse 's level. Ignored in 'convex'. Default value is 0.95.

ellipse.alpha

Alpha for frame specifying the transparency level of fill color. Use alpha = 0 for no fill color.

shape

the shape of points.

pointsize

the size of points

labelsize

font size for the labels

main

plot main title.

xlab, ylab

character vector specifying x and y axis labels, respectively. Use xlab = FALSE and ylab = FALSE to hide xlab and ylab, respectively.

outlier.pointsize, outlier.color, outlier.shape, outlier.labelsize

arguments for customizing outliers, which can be detected only in DBSCAN clustering.

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(), ....

...

other arguments to be passed to the functions ggscatter and ggpar.

Value

return a ggpplot.

Author(s)

Alboukadel Kassambara [e-mail]

See Also

fviz_silhouette, hcut, hkmeans, eclust, fviz_dend

Examples

set.seed(123)

# Data preparation
# +++++++++++++++
data("iris")
head(iris)
# Remove species column (5) and scale the data
iris.scaled <- scale(iris[, -5])

# K-means clustering
# +++++++++++++++++++++
km.res <- kmeans(iris.scaled, 3, nstart = 10)

# Visualize kmeans clustering
# use repel = TRUE to avoid overplotting
fviz_cluster(km.res, iris[, -5], ellipse.type = "norm")


# Change the color palette and theme
fviz_cluster(km.res, iris[, -5],
   palette = "Set2", ggtheme = theme_minimal())

 ## Not run: 
# Show points only
fviz_cluster(km.res, iris[, -5], geom = "point")
# Show text only
fviz_cluster(km.res, iris[, -5], geom = "text")

# PAM clustering
# ++++++++++++++++++++
require(cluster)
pam.res <- pam(iris.scaled, 3)
 # Visualize pam clustering
fviz_cluster(pam.res, geom = "point", ellipse.type = "norm")

# Hierarchical clustering
# ++++++++++++++++++++++++
# Use hcut() which compute hclust and cut the tree
hc.cut <- hcut(iris.scaled, k = 3, hc_method = "complete")
# Visualize dendrogram
fviz_dend(hc.cut, show_labels = FALSE, rect = TRUE)
# Visualize cluster
fviz_cluster(hc.cut, ellipse.type = "convex")


## End(Not run)