Chapter 9

Visualizing Dendorgrams

# Lets load the data first
data(USArrests)

# Computer distances and hierarchical clustering
dd <- dist(scale(USArrests), method = "euclidean")
hc <- hclust(dd, method = "ward.D2")

#Lets install the necessary packages
library(factoextra)

## Loading required package: ggplot2

## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa

fviz_dend(hc, cex = 0.5)

## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
## of ggplot2 3.3.4.
## ℹ The deprecated feature was likely used in the factoextra package.
##   Please report the issue at <https://github.com/kassambara/factoextra/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## FViz

fviz_dend(hc, cex = 0.5,
main = "Dendrogram - ward.D2",
xlab = "Objects", ylab = "Distance", sub = "")

drawing horizontal

fviz_dend(hc, cex = 0.5, horiz = TRUE)

Coloring branches and add rectangle

fviz_dend(hc, k = 4, # Cut in four groups
cex = 0.5, # label size
k_colors = c("#2E9FDF", "#00AFBB", "#E7B800", "#FC4E07"),
color_labels_by_k = TRUE, # color labels by groups
rect = TRUE, # Add rectangle around groups
rect_border = "blue",
rect_fill = TRUE)

# change the theme
fviz_dend(hc, k = 4,
            cex = 0.5,
            k_colors = c("#2E9FDF", "#00AFBB", "#E7B800", "#FC4E07"),
            color_labels_by_k = TRUE,
            ggtheme = theme_gray())

change group color using jco

fviz_dend(hc, cex = 0.5, k = 4, k_colors = "jco")

horizontal with rectangles around

fviz_dend(hc, k = 4, cex = 0.4, horiz = TRUE, k_colors = "jco", rect = TRUE, rect_border = "jco", rect_fill = TRUE)

circular dend

fviz_dend(hc, cex=0.5, k = 4, k_colors = "jco", type = "circular")

Phylogeny Tree

require("igraph")

## Loading required package: igraph

## 
## Attaching package: 'igraph'

## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum

## The following object is masked from 'package:base':
## 
##     union

fviz_dend(hc, k = 4, k_colors = "jco", type = "phylogenic", repel = TRUE)

lets try the layout.gem

require("igraph")
fviz_dend(hc, k = 4, k_colors = "jco", type = "phylogenic", repel = TRUE, phylo_layout = "layout.gem")

## Zooming in

fviz_dend(hc, xlim = c(1,20), ylim = c(1,8))

Lets break the dendrogram at a given height(h) and lets look at the truncated one

dend_plot <- fviz_dend(hc, k = 4, cex = 0.5, k_colors = "jco")
dend_data <- attr(dend_plot, "dendrogram")
dend_cuts <- cut(dend_data, h = 10)
fviz_dend(dend_cuts$upper)

## Warning in min(-diff(our_dend_heights)): no non-missing arguments to min;
## returning Inf

print(dend_plot)

#CLuster dendrogram

fviz_dend(dend_cuts$lower[[1]], main = "Subtree 1")

fviz_dend(dend_cuts$lower[[2]], main = "Subtree 2")

drawing circular in the second format

fviz_dend(dend_cuts$lower[[2]], type = "circular")

##Saving into pdf

pdf("dendrogram.pdf", width = 30, height = 15)
p <- fviz_dend(hc, k = 4, cex = 1, k_colors = "jco")
print(p)
dev.off()

## png 
##   2

Creat a new dendrogram

data <- scale(USArrests)
dist.res <- dist(data)
hc <- hclust(dist.res, method = "ward.D2")
dend <- as.dendrogram(hc)
plot(dend)

Creating dendromgram chaining order

library(dendextend)

## 
## ---------------------
## Welcome to dendextend version 1.17.1
## Type citation('dendextend') for how to cite the package.
## 
## Type browseVignettes(package = 'dendextend') for the package vignette.
## The github page is: https://github.com/talgalili/dendextend/
## 
## Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
## You may ask questions at stackoverflow, use the r and dendextend tags: 
##   https://stackoverflow.com/questions/tagged/dendextend
## 
##  To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
## ---------------------

## 
## Attaching package: 'dendextend'

## The following object is masked from 'package:stats':
## 
##     cutree

dend <- USArrests[1:5,] %>%
        scale %>%
        dist %>%
        hclust(method = "ward.D2") %>%
        as.dendrogram
plot(dend)        

Using set as an example

library (dendextend)
# 1. Create a customized dendrogram
mycols <- c("#2E9FDF", "#00AFBB", "#E7B800", "#FC4E07")
dend <- as.dendrogram (hc) %>%
        set ("branches_lwd", 1) %>%
        set ("branches_k_color", mycols, k = 4) %>%
        set("labels_colors", mycols, k = 4) %>%
        set ("labels_cex", 0.5)
# 2. Create plot
fviz_dend (dend)