https://github.com/andrie/ggdendro

Tools to extract dendrogram plot data for use with 'ggplot2'
https://github.com/andrie/ggdendro

ggplot2 r r-package r-stats

Last synced: 3 months ago
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Tools to extract dendrogram plot data for use with 'ggplot2'

• Host: GitHub
• URL: https://github.com/andrie/ggdendro
• Owner: andrie
• Created: 2011-08-06T20:35:39.000Z (almost 13 years ago)
• Default Branch: main
• Last Pushed: 2024-02-18T21:28:07.000Z (4 months ago)
• Last Synced: 2024-03-24T21:35:46.563Z (3 months ago)
• Topics: ggplot2, r, r-package, r-stats
• Language: R
• Homepage: http://andrie.github.io/ggdendro/
• Size: 8.3 MB
• Stars: 81
• Watchers: 9
• Forks: 11
• Open Issues: 3
• Metadata Files:
  • Readme: README.Rmd

Lists

• awesome-r-dataviz - ggdendro - Tools to extract dendrogram plot data for use with ggplot. (ggplot / Additional Plot Types)
• awesome-stars - andrie/ggdendro - Tools to extract dendrogram plot data for use with 'ggplot2' (R)
• awesome-ggplot2 - GitHub

README

        
---

output: github_document

format: gfm

default-image-extension: ""

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# ggdendro 

Provides functions for creating dendrograms and tree plots using `ggplot2`.

[![CRAN status](https://www.r-pkg.org/badges/version/ggdendro)](https://CRAN.R-project.org/package=ggdendro)

[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/ggdendro)](http://www.r-pkg.org/pkg/ggdendro)

[![R-CMD-check](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andrie/ggdendro/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/andrie/ggdendro/branch/main/graph/badge.svg)](https://app.codecov.io/gh/andrie/ggdendro?branch=main)

[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)

The `ggdendro` package offers a generic function to extract data and text from the various clustering models:

* `dendro_data()` extracts cluster information from the model object, e.g. cluster allocation, line segment data or label data.

The `dendro_data` object has methods for the following classes:

* `tree`

* `hclust`

* `dendrogram`

* `rpart`

These methods create an object of class `dendro`, which is essentially a list of data frames.  To extract the relevant data frames from the list, use the three accessor functions:

* `segment()` for the line segment data

* `label()` for the text for each end segment

* `leaf_label()` for the leaf labels of a tree diagram

The results of these functions can then be passed to `ggplot()` for plotting.

## Examples

```{r}

library(ggplot2)

library(ggdendro)

hc <- hclust(dist(USArrests), "ave")

hcdata <- dendro_data(hc, type = "rectangle")

ggplot() +

  geom_segment(data = segment(hcdata), 

               aes(x = x, y = y, xend = xend, yend = yend)

  ) +

  geom_text(data = label(hcdata), 

            aes(x = x, y = y, label = label, hjust = 0), 

            size = 3

  ) +

  coord_flip() +

  scale_y_reverse(expand = c(0.2, 0))

### demonstrate plotting directly from object class hclust

ggdendrogram(hc)

ggdendrogram(hc, rotate = TRUE)

### demonstrate converting hclust to dendro using dendro_data first

hcdata <- dendro_data(hc)

ggdendrogram(hcdata, rotate = TRUE) +

  labs(title = "Dendrogram in ggplot2")

```

	    

# Use `dendextend` instead

Most of the functionality in `ggdendro` is included in the excellent `dendextend` package.  In most cases, if you need additional functionality, please use the `dendextend` package instead.

The `ggdendro` package will only get minimal maintenance in future.

Refer to