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# dendextend
**[dendextend website](https://talgalili.github.io/dendextend/) (built using [pkgdown](https://pkgdown.r-lib.org/))**
**Table of contents:**
* [Introduction](#introduction)
* [Installation](#installation)
* [Usage](#usage)
* [Getting help](#getting-help)
* [How to cite the dendextend package](#how-to-cite-the-dendextend-package)
* [Submitting bug reports and patches](#submitting-bug-reports-and-patches)
## Introduction
Class "dendrogram" provides general functions for handling tree-like structures in R. It is intended as a replacement for similar functions in hierarchical clustering and classification/regression trees, such that all of these can use the same engine for plotting or cutting trees.
However, many basic features are still missing from the dendrogram class. This package aims at filling in some gaps.
**The dendextend package extending R core dendrogram functions.**
## Installation
To install and load dendextend, simply use:
```r
install.packages('dendextend') # stable CRAN version
library("dendextend") # load the package
```
## Usage
Vignettes:
* [Introduction to dendextend](https://talgalili.github.io/dendextend/articles/dendextend.html)
* [Frequently asked questions](https://talgalili.github.io/dendextend/articles/FAQ.html)
* [Hierarchical cluster analysis on famous data sets - enhanced with the dendextend package](https://talgalili.github.io/dendextend/articles/Cluster_Analysis.html)
Also ceck out the [dendextend tag in stackoverflow](https://stackoverflow.com/questions/tagged/dendextend) for more examples.
A notable sister package for dendextend is [heatmaply](https://talgalili.github.io/heatmaply/articles/heatmaply.html) for creating interactive cluster heatmaps using R (combining dendextend and plotly).
## Getting help
Please post your question to stackoverflow using the tags: [dendextend](https://stackoverflow.com/questions/tagged/dendextend) and [r](https://stackoverflow.com/questions/tagged/dendextend).
## How to cite the dendextend package
The methods within the code package can be cited as:
Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of
hierarchical clustering. Bioinformatics. DOI: 10.1093/bioinformatics/btv428
A BibTeX entry for LaTeX users is
@Article{,
author = {Tal Galili},
title = {dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering},
journal = {Bioinformatics},
year = {2015},
doi = {10.1093/bioinformatics/btv428},
url = {https://academic.oup.com/bioinformatics/article/31/22/3718/240978/dendextend-an-R-package-for-visualizing-adjusting},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/31/22/3718/17122682/btv428.pdf},
}
This free open-source software implements academic research by the authors and co-workers. If you use
it, please support the project by citing the appropriate journal articles.
## Submitting bug reports and patches
You are welcome to:
* submit bug-reports and features' suggestions at: <https://github.com/talgalili/dendextend/issues>
* send a pull request on: <https://github.com/talgalili/dendextend/>
* compose a friendly e-mail to: <tal.galili@gmail.com>
Before reporting bugs, please make sure you're using the latest version from github:
```R
install.packages.2 <- function (pkg) if (!require(pkg)) install.packages(pkg);
install.packages.2('remotes')
remotes::install_github('talgalili/dendextend')
# Having colorspace is also useful, since it is used
# In various examples in the vignettes
install.packages.2('colorspace')
```
## Latest news
You can see the most recent changes to the package in the [NEWS.md file](https://talgalili.github.io/dendextend/news/index.html)
## Code of conduct
Please note that this project is released with a [Contributor Code of Conduct](https://github.com/talgalili/dendextend/blob/master/CONDUCT.md). By participating in this project you agree to abide by its terms.
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dendextend:扩展R的树状图功能
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树枝状延伸 (使用) 目录: 介绍 类“树状图”提供了处理R中树状结构的通用功能。它旨在替代层次聚类和分类/回归树中的类似功能,因此所有这些功能都可以使用相同的引擎来绘制或切割树。 但是,树状图类仍缺少许多基本功能。 该软件包旨在填补一些空白。 dendextend软件包扩展了R核心树状图功能。 安装 要安装和加载dendextend,只需使用: install.packages( ' dendextend ' ) # stable CRAN version library( " dendextend " ) # load the package 用法 小插图: 另外请查看的获取更多示例。 dendextend的一个值得注意的姐妹包是用于使用R(将dendextend和plotly组合)来创建交互式集群热图。 获得帮助 请使用以下标记将您的问题发布到stackoverflow:
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dendextend:扩展R的树状图功能 (597个子文件)
00Index 73B
dendextend-tutorial.bib 26KB
jss.bst 32KB
ChangeLog 593KB
CITATION 935B
jss.cls 14KB
docsearch.css 11KB
pkgdown.css 7KB
bootstrap-toc.css 2KB
DESCRIPTION 4KB
.gitignore 45B
.gitignore 31B
dendextend.html 193KB
index.html 90KB
Cluster_Analysis.html 85KB
FAQ.html 56KB
set.html 40KB
tanglegram.html 35KB
index.html 35KB
color_branches.html 32KB
colored_dots.html 26KB
colored_bars.html 26KB
cutree-methods.html 22KB
Bk_plot.html 21KB
ggdend.html 21KB
rect.dendrogram.html 21KB
highlight_branches.html 20KB
rotate.html 19KB
branches_attr_by_clusters.html 18KB
index.html 16KB
circlize_dendrogram.html 16KB
cor_cophenetic.html 16KB
entanglement.html 16KB
FM_index.html 16KB
get_nodes_attr.html 16KB
untangle_step_rotate_2side.html 15KB
FM_index_profdpm.html 15KB
cor_bakers_gamma.html 15KB
FM_index_R.html 15KB
FM_index_permutation.html 15KB
plot_horiz.dendrogram.html 15KB
Bk.html 15KB
all.equal.dendrogram.html 14KB
untangle.html 14KB
highlight_distinct_edges.html 14KB
labels-assign.html 14KB
cutree_1k.dendrogram.html 14KB
pvrect2.html 13KB
branches_attr_by_labels.html 13KB
color_labels.html 13KB
pvclust_show_signif.html 13KB
get_subdendrograms.html 13KB
set_labels.html 13KB
untangle_step_rotate_1side.html 13KB
find_k.html 13KB
Bk_permutations.html 12KB
pvclust_show_signif_gradient.html 12KB
assign_values_to_branches_edgePar.html 12KB
sort_levels_values.html 12KB
na_locf.html 12KB
dist.dendlist.html 12KB
Quick_Introduction.html 12KB
find_dend.html 12KB
collapse_branch.html 12KB
identify.dendrogram.html 12KB
cutree_1h.dendrogram.html 12KB
dendlist.html 12KB
match_order_dendrogram_by_old_order.html 12KB
order.dendrogram-assign.html 12KB
noded_with_condition.html 12KB
untangle_random_search.html 12KB
get_nodes_xy.html 12KB
unclass_dend.html 12KB
labels_colors.html 12KB
which_node.html 11KB
branches_attr_by_lists.html 11KB
cor.dendlist.html 11KB
khan.html 11KB
assign_values_to_nodes_nodePar.html 11KB
cut_lower_fun.html 11KB
prune.html 11KB
ladderize.html 11KB
sample.dendrogram.html 11KB
assign_values_to_leaves_nodePar.html 11KB
hang.dendrogram.html 11KB
find_dendrogram.html 11KB
dend_diff.html 11KB
has_component_in_attribute.html 11KB
as.phylo.dendrogram.html 11KB
get_leaves_branches_col.html 11KB
count_terminal_nodes.html 11KB
fix_members_attr.dendrogram.html 11KB
intersect_trees.html 11KB
shuffle.html 11KB
get_leaves_edgePar.html 11KB
heights_per_k.dendrogram.html 11KB
get_leaves_branches_attr.html 11KB
assign_values_to_leaves_edgePar.html 11KB
get_leaves_attr.html 11KB
common_subtrees_clusters.html 10KB
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