# Quick Introduction
Author: Tal Galili
Date: 2015-10-31

#### Tal Galili

#### 2015-10-31

## 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)

    ## [1] 1 2 5 3 4

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

    ## [1] "A"      "B"      "extend" "dend"   "C"

Get/set labels’ colors

    labels_colors(dend)

    ## NULL

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

    ##           A           B      extend        dend           C
    ## "#FF0000FF" "#CCFF00FF" "#00FF66FF" "#0066FFFF" "#CC00FFFF"

    plot(dend)

Cut-tree, and color branches

    cutree(dend, k = 2)

    ##      A      B   dend      C extend
    ##      1      1      2      2      2

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

Sort

    dend2 <- sort(dend)
    plot(dend2)

Compare

    tanglegram( dend,  dend2  )

Cor

    cor_cophenetic( dend,  dend2  )

    ## [1] 1

ggplot2

    library(ggplot2)
    ggplot(dend)

    ## Warning: Removed 9 rows containing missing values (geom_point).

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()