dendextend v1.8.0

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Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Readme

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dendextend

Table of contents:

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.

Motivation

Extending R core dendrogram functions.

Installation

To install the stable version on CRAN:

install.packages('dendextend')
# install.packages('dendextendRcpp')

To install the GitHub version:

install.packages.2 <- function (pkg) if (!require(pkg)) install.packages(pkg);
install.packages.2('devtools')
# install.packages.2('Rcpp')
# make sure you have Rtools installed first! if not, then run:
#install.packages('installr'); install.Rtools()
devtools::install_github('talgalili/dendextend')
# devtools::install_github('talgalili/dendextendRcpp')

# Having colorspace is also useful, since it is used
# In various examples in the vignettes
install.packages.2('colorspace')

And then you may load the package using:

library("dendextend")
# library("dendextendRcpp") # dendextendRcpp is no longer supported (or available on CRAN). Still, dendextend is faster these days, in recent versions of R, thanks to some updates to labels.dendrogram and other modifications to R.

Usage

Vignettes:

Share your dendrograms!

If you have made interesting work using the dendextend package, I would LOVE to know about it. It can be a blog post, an academic paper, or just some plots you made for your work in the industry. Please contact me (see below) with what you have done, and I would also be happy to promote it in this page.

Usages of dendextend

Packages:

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.

Contact

You are welcome to:

Latest news

You can see the most recent changes to the package in the NEWS.md file

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Functions in dendextend

Name Description
Bk_plot Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's
cor_FM_index Correlation of FM_index for some k
cor.dendlist Correlation matrix between a list of trees.
d3dendro_options Get or set current defaults for d3dendrogram
d3dendrogram Plot dendrogram to webpage and view.
dist.dendlist Topological Distances Between Two dendrograms
dist_long Turns a dist object to a "long" table
get_leaves_attr Get/set attributes of dendrogram's leaves
get_leaves_branches_attr Get an attribute of the branches of a dendrogram's leaves
get_subdendrograms Extract a list of k subdendrograms from a given dendrogram object
ggdend Creates dendrogram plot using ggplot.
khan Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
labels<- "label" assignment operator
nleaves Counts the number of leaves in a tree
rank_branches Rank branches' heights
nnodes Counts the number of nodes (Vertices) in a tree
rank_order.dendrogram Fix rank of leaves order values in a dendrogram
remove_branches_edgePar Remove all edgePar values from a dendrogram's branches
remove_leaves_nodePar Remove all nodePar values from a dendrogram's leaves
tanglegram Tanglegram plot
theme_dendro Creates completely blank theme in ggplot
untangle_step_rotate_2side Stepwise untangle two trees one at a time
all.equal.dendrogram Global Comparison of two (or more) dendrograms
all_couple_rotations_at_k Rotate tree branches for k
Bk Bk - Calculating Fowlkes-Mallows Index for two dendrogram
which_leaf Which node is a leaf?
Bk_permutations Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram
as.dendlist Try to coerce something into a dendlist
all_unique Check if all the elements in a vector are unique
as.phylo.dendrogram Convert a dendrogram into phylo
click_rotate Interactively rotate a tree object
collapse_branch Collapse branches under a tolerance level
cor_bakers_gamma Baker's Gamma correlation coefficient
cor_common_nodes Proportion of commong nodes between two trees
as_hclust_fixed Convert dendrogram Objects to Class hclust
branches_attr_by_clusters Change col/lwd/lty of branches based on clusters
dendlist Creating a dendlist object from several dendrograms
branches_attr_by_labels Change col/lwd/lty of branches matching labels condition
FM_index_profdpm Calculating Fowlkes-Mallows index using the profdpm R package
FM_index_permutation Calculating Fowlkes-Mallows Index under H0
dendextend_labels.dendrogram Labels of the Leaves in a Dendrogram
assign_values_to_leaves_nodePar Assign values to nodePar of dendrogram's leaves
color_labels Color dend's labels according to sub-clusters
dend_expend Finds a "good" dendrogram for a dist
dendextend_options Access to dendextend_options
color_branches Color tree's branches according to sub-clusters
count_terminal_nodes Counts the number of terminal nodes (merging 0 nodes!)
cor_cophenetic Cophenetic correlation between two trees
assign_values_to_leaves_edgePar Assign values to edgePar of dendrogram's leaves
colored_dots Add colored dots beside a dendrogram
find_dendrogram Search for the subdendrogram structure composed of indicated labels
get_branches_heights Get height attributes from a dendrogram
common_subtrees_clusters Find clusters of common subtrees
dend_diff Plots two trees side by side, highlighting edges unique to each tree in red.
get_childrens_heights Get height attributes from a dendrogram's children
min_depth Find minimum/maximum depth of a dendrogram
find_k Find the (estimated) number of clusters for a dendrogram using average silhouette width
fix_members_attr.dendrogram Fix members attr in a dendrogram
entanglement Measures entanglement between two trees
dendextend-package Functions for extending dendrogram objects
get_leaves_edgePar Get edgePar of dendrogram's leaves
get_leaves_branches_col Get the colors of the branches of a dendrogram's leaves
hang.dendrogram Hang dendrogram leaves
heights_per_k.dendrogram Which height will result in which k for a dendrogram
highlight_branches_col Highlight a dendrogram's branches heights via color and line-width
fac2num Turns a factor into a number
has_component_in_attribute Does a dendrogram has an edgePar/nodePar component?
ladderize Ladderize a Tree
leaf_Colors Return the leaf Colors of a dendrogram
labels_cex Retrieve/assign cex to the labels of a dendrogram
order.hclust Ordering of the Leaves in a hclust Dendrogram
get_leaves_nodePar Get nodePar of dendrogram's leaves
highlight_distinct_edges Highlight distint edges in a tree (compared to another one)
get_nodes_attr Get attributes of dendrogram's nodes
identify.dendrogram Identify Clusters in a Dendrogram (not hclust)
is_null_list Checks if the value is and empty list()
is_some_class Is the object of some class
noded_with_condition Find which nodes satisfies a condition
order.dendrogram<- order.dendrogram<- assignment operator
labels_colors Retrieve/assign colors to the labels of a dendrogram
partition_leaves A list with labels for each subtree (edge)
pvrect2 Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values
lowest_common_branch Find lowest common branch were the two items are shared
FM_index Calculating Fowlkes-Mallows Index
match_order_by_labels Adjust the order of one dendrogram based on another (using labels)
plot_horiz.dendrogram Plotting a left-tip-adjusted horizontal dendrogram
prune Prunes a tree (using leaves' labels)
raise.dendrogram Raise the height of a dendrogram tree
rotate_DendSer Rotates dend based on DendSer
reexports Objects exported from other packages
rotate Rotate a tree object
prune_common_subtrees.dendlist Prune trees to their common subtrees
FM_index_R Calculating Fowlkes-Mallows index in R
assign_values_to_nodes_nodePar Assign values to nodePar of dendrogram's nodes
sort_dist_mat Sorts a distance matrix by rows and columns names
bakers_gamma_for_2_k_matrix Bakers Gamma for two k matrices
prune_leaf Trims one leaf from a dendrogram
color_unique_labels Color unique labels in a dendrogram
reindex_dend Reindexing a pruned dendrogram
rank_values_with_clusters Rank a vector based on clusters
colored_bars Add colored bars to a dendrogram
rect.dendrogram Draw Rectangles Around a Dendrogram's Clusters
sort_levels_values Sort the values level in a vector
untangle untangle dendrograms
sort_2_clusters_vectors Sorts two clusters vector by their names
untangle_DendSer Tries to run DendSer on a dendrogram
unbranch unbranch trees
shuffle Random rotation of trees
cut_lower_fun Cut a dendrogram - and run a function on the output
unclass_dend unclass an entire dendrogram tree
cutree Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree_1h.dendrogram cutree for dendrogram (by 1 height only!)
set_labels Set/place new labels in a dendrogram
cutree_1k.dendrogram cutree for dendrogram (by 1 k value only!)
set Set (/update) features to a dendrogram
duplicate_leaf Duplicate a leaf X times
distinct_edges Finds distinct edges in one tree compared to another
untangle_random_search Untangle - random search
flatten.dendrogram Flatten the branches of a dendrogram's root
untangle_step_rotate_1side Stepwise untangle one tree compared to another
flip_leaves Flip leaves
get_root_branches_attr get attributes from the dendrogram's root(!) branches
get_nodes_xy Get the x-y coordinates of a dendrogram's nodes
intersect_trees Intersect trees
is.natural.number Check if numbers are natural
match_order_dendrogram_by_old_order Adjust the order of one dendrogram based on another (using order)
na_locf Last Observation Carried Forward
pvclust_show_signif The significant branches in a dendrogram, based on a pvclust object
pvclust_show_signif_gradient Significance gradient of branches in a dendrogram (via pvclust)
remove_nodes_nodePar Remove all nodePar values from a dendrogram's nodes
rllply recursivly apply a function on a list
sample.dendrogram Sample a tree
seriate_dendrogram Rotates a dendrogram based on a seriation of a distance matrix
which_node Which node id is common to a group of labels
branches_attr_by_lists Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members
circlize_dendrogram Plot a circlized dendrograms
assign_dendextend_options Populates dendextend functions into dendextend_options
assign_values_to_branches_edgePar Assign values to edgePar of dendrogram's branches
DendSer.dendrogram Tries to run DendSer on a dendrogram
No Results!

Vignettes of dendextend

Name
disabled/dendextend-tutorial.rnw
Cluster_Analysis.Rmd
FAQ.Rmd
Quick_Introduction.Rmd
introduction.Rmd
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