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dendextend (version 1.1.2)

Extending R's Dendrogram Functionality

Description

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.

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Install

install.packages('dendextend')

Monthly Downloads

76,670

Version

1.1.2

License

GPL-2 | GPL-3

Issues

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Repository

https://github.com/talgalili/dendextend/

Homepage

http://cran.r-project.org/package=dendextend

Maintainer

Tal Galili

Last Published

October 31st, 2015

Functions in dendextend (1.1.2)

raise.dendrogram

Raise the height of a dendrogram tree

Checks if an object is of class dendlist

Add colored bars to a dendrogram

Interactively rotate a tree object

cutree_1h.dendrogram

cutree for dendrogram (by 1 height only!)

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

Ladderize a Tree

"label" assignment operator

noded_with_condition

Find which nodes satisfies a condition

Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.

Bk_permutations

Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram

Color dend's labels according to sub-clusters

get_branches_heights

Get height attributes from a dendrogram

plot_horiz.dendrogram

Plotting a left-tip-adjusted horizontal dendrogram

Prunes a tree (using leaves' labels)

assign_values_to_nodes_nodePar

Assign values to nodePar of dendrogram's nodes

untangle_DendSer

Tries to run DendSer on a dendrogram

highlight_distinct_edges

Highlight distint edges in a tree (compared to another one)

get_childrens_heights

Get height attributes from a dendrogram's children

Topological Distances Between Two dendrograms

common_subtrees_clusters

Find clusters of common subtrees

Trimms one leaf from a dendrogram

intersect_trees

Intersect trees

branches_attr_by_labels

Change col/lwd/lty of branches matching labels condition

Color tree's branches according to sub-clusters

DendSer.dendrogram

Tries to run DendSer on a dendrogram

Plots two trees side by side, highlighting edges unique to each tree in red.

unclass an entire dendrogram tree

dendextend-package

Functions for extending dendrogram objects

Ordering of the Leaves in a hclust Dendrogram

Cut a dendrogram - and run a function on the output

rank_order.dendrogram

Fix rank of leaves order values in a dendrogram

all_couple_rotations_at_k

Rotate tree branches for k

Check if all the elements in a vector are unique

remove_nodes_nodePar

Remove all nodePar values from a dendrogram's nodes

Rotate a tree object

Counts the number of nodes (Vertices) in a tree

hang.dendrogram

Hang dendrogram leaves

Try to coerce something into a dendlist

fix_members_attr.dendrogram

Fix members attr in a dendrogram

remove_branches_edgePar

Remove all edgePar values from a dendrogram's branches

is.natural.number

Check if numbers are natural

Measures entanglement between two trees

assign_values_to_branches_edgePar

Assign values to edgePar of dendrogram's branches

assign_dendextend_options

Populates dendextend functions into dendextend_options

Retrieve/assign cex to the labels of a dendrogram

Sorts a distance matrix by rows and columns

Get the x-y coordiantes of a dendrogram's nodes

assign_values_to_leaves_nodePar

Assign values to nodePar of dendrogram's leaves

sort_levels_values

Sort the values level in a vector

untangle_step_rotate_1side

Stepwise untangle one tree compared to another

Get attributes of dendrogram's nodes

rect.dendrogram

Draw Rectangles Around a Dendrogram's Clusters

prune_common_subtrees.dendlist

Prune trees to their common subtrees

untangle_random_search

Untangle - random search

Rotates dend based on DendSer

Set (/update) features to a dendrogram

recursivly apply a function on a list

get_leaves_branches_col

Get the colors of the branches of a dendrogram's leaves

FM_index_profdpm

Calculating Fowlkes-Mallows index using the profdpm R package

all.equal.dendrogram

Global Comparison of two (or more) dendrograms

untangle dendrograms

lowest_common_branch

Find lowest common branch were the two items are shared

match_order_by_labels

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

cor_bakers_gamma

Baker's Gamma correlation coefficient

Bk - Calculating Fowlkes-Mallows Index for two dendrogram

flatten.dendrogram

Flatten the branches of a dendrogram's root

as.phylo.dendrogram

Convert a dendrogram into phylo

get_leaves_branches_attr

Get an attribute of the branches of a dendrogram's leaves

Pipe an object forward into a function call/expression.

Tanglegram plot

Turns a dist object to a "long" table

Calculating Fowlkes-Mallows Index

Creating a dendlist object from several dendrograms

assign_values_to_leaves_edgePar

Assign values to edgePar of dendrogram's leaves

Is the object of class dendrogram

count_terminal_nodes

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

collapse_branch

Collapse branches under a tolerance level

sample.dendrogram

Creates dendrogram plot using ggplot.

Plot dendrogram to webpage and view.

match_order_dendrogram_by_old_order

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

rank_values_with_clusters

Rank a vector based on clusters

get_leaves_nodePar

Get nodePar of dendrogram's leaves

pvclust_show_signif

Shows the significant branches in a dendrogram, based on a pvclust object

Is the object of class phylo

Checks if the value is and empty list()

Retrieve/assign colors to the labels of a dendrogram

sort_2_clusters_vectors

Sorts two clusters vector by their names

Which node id is common to a group of labels

get_leaves_edgePar

Get edgePar of dendrogram's leaves

bakers_gamma_for_2_k_matrix

Bakers Gamma for two k matrices

d3dendro_options

Get or set current defaults for d3dendrogram

as_hclust_fixed

Convert dendrogram Objects to Class hclust

remove_leaves_nodePar

Remove all nodePar values from a dendrogram's leaves

Cophenetic correlation between two trees

Turns a factor into a number

Is the object of class hclust

Counts the number of leaves in a tree

partition_leaves

A list with labels for each subtree (edge)

Creates completely blank theme in ggplot

FM_index_permutation

Calculating Fowlkes-Mallows Index under H0

Correlation matrix between a list of trees.

pvclust_show_signif_gradient

Shows the gradient of significance of branches in a dendrogram, based on a pvclust object

untangle_step_rotate_2side

Stepwise untangle two trees one at a time

cutree_1k.dendrogram

cutree for dendrogram (by 1 k value only!)

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

Return the leaf Colors of a dendrogram

Random rotation of trees

dendextend_labels.dendrogram

Labels of the Leaves in a Dendrogram

circlize_dendrogram

Plot a circlized dendrograms

get_leaves_attr

Get/set attributes of dendrogram's leaves

get_root_branches_attr

get attributes from the dendrogram's root(!) branches

Last Observation Carried Forward

Correlation of FM_index for some k

Duplicate a leaf X times

identify.dendrogram

Identify Clusters in a Dendrogram (not hclust)

order.dendrogram<-

order.dendrogram<- assignment operator

Which node is a leaf?

cor_common_nodes

Proportion of commong nodes between two trees

branches_attr_by_clusters

Change col/lwd/lty of branches based on clusters

heights_per_k.dendrogram

Which height will result in which k for a dendrogram

Rank branches' heights

dendextend_options

Access to dendextend_options

Finds the edges present in the first tree but not in the second

Calculating Fowlkes-Mallows index in R