1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
## ---- echo = FALSE, message = FALSE, warning=FALSE----------------------------
library(dendextend)
library(knitr)
knitr::opts_chunk$set(
cache = TRUE,
dpi = 75,
fig.width = 6, fig.height = 6,
# comment = "#>",
tidy = FALSE)
# https://stackoverflow.com/questions/24091735/why-pandoc-does-not-retrieve-the-image-file
# < ! -- rmarkdown v1 -->
## -----------------------------------------------------------------------------
library(dendextend) #
## -----------------------------------------------------------------------------
dend <- c(1:5) %>% dist %>% hclust("ave") %>% as.dendrogram
## -----------------------------------------------------------------------------
plot(dend)
## -----------------------------------------------------------------------------
labels(dend)
labels(dend) <- c("A", "B", "extend", "dend", "C")
labels(dend)
## -----------------------------------------------------------------------------
labels_colors(dend)
labels_colors(dend) <- rainbow(5)
labels_colors(dend)
plot(dend)
## -----------------------------------------------------------------------------
cutree(dend, k = 2)
dend <- color_branches(dend, k = 2)
plot(dend)
## -----------------------------------------------------------------------------
dend2 <- sort(dend)
plot(dend2)
## -----------------------------------------------------------------------------
tanglegram( dend, dend2 )
## -----------------------------------------------------------------------------
cor_cophenetic( dend, dend2 )
## -----------------------------------------------------------------------------
library(ggplot2)
ggplot(dend)
## -----------------------------------------------------------------------------
# library(plotly)
# set_credentials_file(...)
# you'll need to get it from here: https://plot.ly/ggplot2/getting-started/
# ggplot(dend)
# py <- plotly()
# py$ggplotly()
|
