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---
title: "Quick Introduction"
date: "`r Sys.Date()`"
author: "Tal Galili"
output:
html_vignette:
toc: yes
editor_options:
chunk_output_type: console
---
<!--
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{A quick introduction to dendextend (start here)}
-->
```{r, echo = FALSE, message = FALSE, warning=FALSE}
library(dendextend)
library(knitr)
knitr::opts_chunk$set(
cache = TRUE,
dpi = 75,
fig.width = 6, fig.height = 6,
# comment = "#>",
tidy = FALSE)
# https://stackoverflow.com/questions/24091735/why-pandoc-does-not-retrieve-the-image-file
# < ! -- rmarkdown v1 -->
```
Start
------------------------------
Load:
```{r}
library(dendextend) #
```
Create a dendrogram (if you don't know what `%>%` is, read about it [here](https://CRAN.R-project.org/package=magrittr/vignettes/magrittr.html) ) :
```{r}
dend <- c(1:5) %>% dist %>% hclust("ave") %>% as.dendrogram
```
Plot:
```{r}
plot(dend)
```
Get/set labels
```{r}
labels(dend)
labels(dend) <- c("A", "B", "extend", "dend", "C")
labels(dend)
```
Get/set labels' colors
```{r}
labels_colors(dend)
labels_colors(dend) <- rainbow(5)
labels_colors(dend)
plot(dend)
```
Cut-tree, and color branches
```{r}
cutree(dend, k = 2)
dend <- color_branches(dend, k = 2)
plot(dend)
```
Sort
```{r}
dend2 <- sort(dend)
plot(dend2)
```
Compare
```{r}
tanglegram( dend, dend2 )
```
Cor
```{r}
cor_cophenetic( dend, dend2 )
```
ggplot2
```{r}
library(ggplot2)
ggplot(dend)
```
Send to plot.ly
```{r}
# library(plotly)
# set_credentials_file(...)
# you'll need to get it from here: https://plot.ly/ggplot2/getting-started/
# ggplot(dend)
# py <- plotly()
# py$ggplotly()
```
|
