factoextra (version 1.0.5)

fviz_dend: Enhanced Visualization of Dendrogram

Description

Draws easily beautiful dendrograms using either R base plot or ggplot2. Provides also an option for drawing a circular dendrogram and phylogenic trees.

Usage

fviz_dend(x, k = NULL, h = NULL, k_colors = NULL, palette = NULL,
  show_labels = TRUE, color_labels_by_k = TRUE, label_cols = NULL,
  labels_track_height = NULL, repel = FALSE, lwd = 0.7,
  type = c("rectangle", "circular", "phylogenic"),
  phylo_layout = "layout.auto", rect = FALSE, rect_border = "gray",
  rect_lty = 2, rect_fill = FALSE, lower_rect, horiz = FALSE, cex = 0.8,
  main = "Cluster Dendrogram", xlab = "", ylab = "Height", sub = NULL,
  ggtheme = theme_classic(), ...)

Arguments

x

an object of class dendrogram, hclust, agnes, diana, hcut, hkmeans or HCPC (FactoMineR).

k

the number of groups for cutting the tree.

h

a numeric value. Cut the dendrogram by cutting at height h. (k overrides h)

k_colors, palette

a vector containing colors to be used for the groups. It should contains k number of colors. Allowed values include also "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

show_labels

a logical value. If TRUE, leaf labels are shown. Default value is TRUE.

color_labels_by_k

logical value. If TRUE, labels are colored automatically by group when k != NULL.

label_cols

a vector containing the colors for labels.

labels_track_height

a positive numeric value for adjusting the room for the labels. Used only when type = "rectangle".

repel

logical value. Use repel = TRUE to avoid label overplotting when type = "phylogenic".

lwd

a numeric value specifying branches and rectangle line width.

type

type of plot. Allowed values are one of "rectangle", "triangle", "circular", "phylogenic".

phylo_layout

the layout to be used for phylogenic trees. Default value is "layout.auto". Allowed values include: layout.auto, layout_with_drl, layout_as_tree, layout.gem, layout.mds and layout_with_lgl.

rect

logical value specifying whether to add a rectangle around groups. Used only when k != NULL.

rect_border, rect_lty

border color and line type for rectangles.

rect_fill

a logical value. If TRUE, fill the rectangle.

lower_rect

a value of how low should the lower part of the rectangle around clusters. Ignored when rect = FALSE.

horiz

a logical value. If TRUE, an horizontal dendrogram is drawn.

cex

size of labels

main, xlab, ylab

main and axis titles

sub

Plot subtitle. If NULL, the method used hierarchical clustering is shown. To remove the subtitle use sub = "".

ggtheme

function, ggplot2 theme name. Default value is theme_classic(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

other arguments to be passed to the function plot.dendrogram()

Value

an object of class fviz_dend which is a ggplot with the attributes "dendrogram" accessible using attr(x, "dendrogram"), where x is the result of fviz_dend().

Examples

# NOT RUN {
# Load and scale the data
data(USArrests)
df <- scale(USArrests)

# Hierarchical clustering
res.hc <- hclust(dist(df))

# Default plot
fviz_dend(res.hc)

# Cut the tree
fviz_dend(res.hc, cex = 0.5, k = 4, color_labels_by_k = TRUE)

# Don't color labels, add rectangles
fviz_dend(res.hc, cex = 0.5, k = 4, 
 color_labels_by_k = FALSE, rect = TRUE)
 
# Change the color of tree using black color for all groups
# Change rectangle border colors
fviz_dend(res.hc, rect = TRUE, k_colors ="black",
rect_border = 2:5, rect_lty = 1)

# Customized color for groups
fviz_dend(res.hc, k = 4, 
 k_colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A"))
 
 
 # Color labels using k-means clusters
 km.clust <- kmeans(df, 4)$cluster
 fviz_dend(res.hc, k = 4, 
   k_colors = c("blue", "green3", "red", "black"),
   label_cols =  km.clust[res.hc$order], cex = 0.6)

# }