Visualize Clustering Results

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. When stand = TRUE, the plotting data must remain finite after scaling.

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(),
  max.points = NULL,
  sample.seed = 123,
  ...
)

Arguments

object: an object of class "partition" created by pam(), clara(), or fanny() [cluster]; "kmeans" [stats]; "dbscan" [fpc]; "Mclust" [mclust]; or "hkmeans" or "eclust" [factoextra]. A custom list may instead contain data plus either cluster or clustering. When the assignments and the data both carry complete, unique, matching names, the assignments are aligned to the data rows by name; otherwise they are used in their given (positional) order. The exception is a clustering fitted from dissimilarities and plotted with external data: complete, unique, non-matching name sets are rejected because positional use would attach clusters to the wrong observations.
data: the data used for clustering. It is required for kmeans and dbscan objects, and for partition or hcut objects fitted from dissimilarities when those objects do not retain the original observations.
choose.vars: a character vector containing variables to be considered for plotting.
stand: logical value; if TRUE, data is standardized before principal component analysis. If scaling produces NA values, fviz_cluster() stops with a package-level error.
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: logical; whether to use ggrepel to avoid overplotting text labels. The old jitter argument is kept for backward compatibility and is converted to repel = TRUE with a deprecation warning.
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. The default is set by each function's ggtheme argument; see the function usage for the actual default. Set ggtheme = NULL to skip applying a ggpubr theme, so the plot keeps ggplot2 default theme or the theme set globally via theme_set(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....
max.points: integer or NULL. When the data has more than max.points observations, a random subset of that many points is drawn so the cluster plot stays readable instead of over-plotting. Only the drawn scatter/labels are thinned: the cluster frame (convex hull / ellipse) and centres are still computed on the full data, so a convex hull is not shrunk by dropping the extreme points a random draw tends to lose. The draw is stratified by cluster so every cluster keeps at least a minimum number of points, and a message reports how many are shown. Any DBSCAN/Mclust outliers are always drawn. The subset is reproducible (see sample.seed) and does not change the caller's random stream. NULL (default) draws every observation.
sample.seed: the random seed used to pick the max.points subset, for a reproducible figure. Ignored when max.points is NULL.
...: other arguments to be passed to the functions ggscatter and ggpar.

Value

a ggplot2 object.

Author

Alboukadel Kassambara alboukadel.kassambara@gmail.com

Examples

set.seed(123)

# Data preparation
# +++++++++++++++
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
# 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())


 if (FALSE) { # \dontrun{
# Show points only
fviz_cluster(km.res, iris[, -5], geom = "point")
# Show text only
fviz_cluster(km.res, iris[, -5], geom = "text")

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

# Hierarchical clustering
# ++++++++++++++++++++++++
# Use hcut(), which computes hclust and cuts 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")

} # }

Usage

Arguments

Value

See also

Author

Examples