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dendextend (version 0.16.1)

Extending R's dendrogram functionality

Description

Functions and methods for extending dendrogram objects in R.

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Install

install.packages('dendextend')

Monthly Downloads

76,670

Version

0.16.1

License

GPL-2 | GPL-3

Issues

59

Pull Requests

2

Stars

159

Forks

31

Maintainer

Tal Galili

Last Published

July 26th, 2014

Functions in dendextend (0.16.1)

Bk

Bk - Calculating Fowlkes-Mallows Index for two dendrogram
FM_index_profdpm

Calculating Fowlkes-Mallows index using the profdpm R package
count_terminal_nodes

Counts the number of terminal nodes (merging 0 nodes!)
FM_index_permutation

Calculating Fowlkes-Mallows Index under H0
assign_values_to_branches_edgePar

Assign values to edgePar of dendrogram's branches
is.phylo

Is the object of class phylo
as_hclust_fixed

Convert dendrogram Objects to Class hclust
bakers_gamma_for_2_k_matrix

Bakers Gamma for two k matrices
plot_horiz.dendrogram

Plotting a left-tip-adjusted horizontal dendrogram
Bk_plot

Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's
rank_branches

Rank branches' heights
is.natural.number

Check if numbers are natural
as.dendlist

Try to coerce something into a dendlist
tanglegram

Tanglegram plot
which_leaf

Which node is a leaf?
rank_order.dendrogram

Fix rank of leaves order values in a dendrogram
leaf_Colors

Return the leaf Colors of a dendrogram
shuffle

Random rotation of trees
order.hclust

Ordering of the Leaves in a hclust Dendrogram
intersect_trees

Intersect trees
prune_leaf

Trimms one leaf from a dendrogram
cut_lower_fun

Cut a dendrogram - and run a function on the output
match_order_by_labels

Adjust the order of one dendrogram based on another (using labels)
DendSer.dendrogram

Tries to run DendSer on a dendrogram
FM_index

Calculating Fowlkes-Mallows Index
cutree_1k.dendrogram

cutree for dendrogram (by 1 k value only!)
nnodes

Counts the number of nodes (Vertices) in a tree
cor_cophenetic

Cophenetic correlation between two trees
branches_attr_by_labels

Change col/lwd/lty of branches matching labels condition
na_locf

Last Observation Carried Forward
sort_levels_values

Sort the values level in a vector
get_branches_attr

get attributes from the dendrogram's root branches
nleaves

Counts the number of leaves in a tree
match_order_dendrogram_by_old_order

Adjust the order of one dendrogram based on another (using order)
dendextend_options

Access to dendextend_options
rotate

Rotate a tree object
sort_dist_mat

Sorts a distance matrix by rows and columns
flip_leaves

Flip leaves
flatten.dendrogram

Flatten the branches of a dendrogram's root
get_nodes_attr

Get attributes of dendrogram's nodes
dendlist

Creating a dendlist object from several dendrograms
rect.dendrogram

Draw Rectangles Around a Dendrogram's Clusters
identify.dendrogram

Identify Clusters in a Dendrogram (not hclust)
order.dendrogram<-

order.dendrogram<- assignment operator
untangle_DendSer

Tries to run DendSer on a dendrogram
colored_bars

Add colored bars to a dendrogram
untangle

untangle dendrograms
rllply

recursivly apply a function on a list
dendextend-package

Functions for extending dendrogram objects
is.dendrogram

Is the object of class dendrogram
get_branches_heights

Get height attributes from a dendrogram
unbranch

unbranch trees
sort_2_clusters_vectors

Sorts two clusters vector by their names
Bk_permutations

Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram
prune

Prunes a tree (using leaves' labels)
unclass_dend

unclass an entire dendrogram tree
noded_with_condition

Find which nodes satisfies a condition
fac2num

Turns a factor into a number
assign_dendextend_options

Populates dendextend functions into dendextend_options
hang.dendrogram

Hang dendrogram leaves
color_branches

Color tree's branches according to sub-clusters
get_leaves_attr

Get/set attributes of dendrogram's leaves
fix_members_attr.dendrogram

Fix members attr in a dendrogram
is_null_list

Checks if the value is and empty list()
heights_per_k.dendrogram

Which height will result in which k for a dendrogram
FM_index_R

Calculating Fowlkes-Mallows index in R
color_labels

Color tree's labels according to sub-clusters
labels<-

"label" assignment operator
labels_colors

Retrieve/assign colors to the labels of a dendrogram
untangle_step_rotate_2side

Stepwise untangle two trees one at a time
raise.dendrogram

Raise the height of a dendrogram tree
branches_attr_by_clusters

Change col/lwd/lty of branches based on clusters
remove_branches_edgePar

Remove all edgePar values from a dendrogram's branches
cutree

Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
is.dendlist

Checks if an object is of class dendlist
lowest_common_branch

Find lowest common branch were the two items are shared
untangle_random_search

Untangle - random search
cor_bakers_gamma

Baker's Gamma correlation coefficient
click_rotate

Interactively rotate a tree object
all_couple_rotations_at_k

Rotate tree branches for k
set

Set (/update) features to a dendrogram
assign_values_to_leaves_nodePar

Assign values to nodePar of dendrogram's leaves
%>%

Pipe an object forward into a function call/expression.
remove_leaves_nodePar

Remove all nodePar values from a dendrogram's leaves
entanglement

Measures entanglement between two trees
get_childrens_heights

Get height attributes from a dendrogram's children
rotate_DendSer

Rotates dend based on DendSer
untangle_step_rotate_1side

Stepwise untangle one tree compared to another
cutree_1h.dendrogram

cutree for dendrogram (by 1 height only!)
plot.dendlist

A plot S3 method for dendlist
duplicate_leaf

Duplicate a leaf X times
sample.dendrogram

Sample a tree
is.hclust

Is the object of class hclust