utput named as order of the hclust function is a vector of the

ts to appear in a hanging tree from the left side to the right side.

wing code was used to examine how the 20 amino acids were

nto a tree,

print(model$order)

utput order of the hclust function for this data set is shown

2.3.

Table 2.3. The output order of hclust for the 20 amino acids.

F

I

L

G

S

Q

H

A

T

14

10

11

8

16

6

9

1

17

E

D

P

K

R

Y

C

M

V

7

4

15

12

2

19

5

13

20

utput named as merge of the hclust function is a matrix of N

and two columns, i.e., (N − 1) × 2 for N data points. The output

height of the hclust function is a vector of N − 1 values

g N − 1 merging heights. A subtree is such a data structure, which

of the tree below a branch node including the root node. Such a

s called a lower-rank subtree. For instance the subtree of the

ids F, I, L is a lower-rank tree of the subtree of the amino acids

nd L in Figure 2.17. Note that a subtree is also a meta data during

ng process. A subtree can either be a single data point such as the

id R or a lower-rank subtree.

The outputs merge and height of the hclust function for a model

for the 20 amino acids. ‘Step’ stands for the merging steps. ‘Left’ stands for a

subtree or an amino acid to be joined to form a higher-rank subtree. ‘Right’

right lower-rank subtree or an amino acid to be joined. ‘Height’ stands for the

subtree.

Step

Left

Right

Height

1)

–2

–19

0.06697225

2)

–3

–7

0.11060656

3)

–6

–9

0.12917607