Quick Introduction"

library(dendextend)
library(knitr)
knitr::opts_chunk$set(
   cache = TRUE,
   dpi = 75,
   fig.width = 6, fig.height = 6,
  # comment = "#>",
  tidy = FALSE)

# http://stackoverflow.com/questions/24091735/why-pandoc-does-not-retrieve-the-image-file
# < ! -- rmarkdown v1 -->

Start

Load:

library(dendextend)

Create a dendrogram (if you don't know what %>% is, read about it here ) :

dend <- c(1:5) %>% dist %>% hclust("ave") %>% as.dendrogram

Plot:

plot(dend)

Get/set labels

labels(dend)
labels(dend) <- c("A", "B", "extend", "dend", "C")
labels(dend)

Get/set labels' colors

labels_colors(dend)
labels_colors(dend) <- rainbow(5)
labels_colors(dend)
plot(dend)

Cut-tree, and color branches

cutree(dend, k = 2)
dend <- color_branches(dend, k = 2)
plot(dend)

Sort

dend2 <- sort(dend)
plot(dend2)

Compare

tanglegram( dend,  dend2  )

Cor

cor_cophenetic( dend,  dend2  )

ggplot2

library(ggplot2)
ggplot(dend) 

Send to plot.ly

# 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()


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dendextend documentation built on Oct. 19, 2018, 9:03 a.m.