dendextend

Bk - Calculating Fowlkes-Mallows Index for two dendrogram

Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram

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

Tries to run DendSer on a dendrogram

Calculating Fowlkes-Mallows Index

Calculating Fowlkes-Mallows index in R

Calculating Fowlkes-Mallows Index under H0

Global Comparison of two (or more) dendrograms

Rotate tree branches for k

Check if all the elements in a vector are unique

Try to coerce something into a dendlist

Convert a dendrogram into phylo

Convert dendrogram Objects to Class hclust

Populates dendextend functions into dendextend_options

Assign values to edgePar of dendrogram's branches

Assign values to edgePar of dendrogram's leaves

Assign values to nodePar of dendrogram's leaves

Assign values to nodePar of dendrogram's nodes

Bakers Gamma for two k matrices

Change col/lwd/lty of branches based on clusters

Change col/lwd/lty of branches matching labels condition

Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members

Plot a circlized dendrograms

Interactively rotate a tree object

Collapse branches under a tolerance level

Color tree's branches according to sub-clusters

Color dend's labels according to sub-clusters

Color unique labels in a dendrogram

Add colored bars to a dendrogram

Add colored dots beside a dendrogram

Find clusters of common subtrees

Correlation matrix between a list of trees.

Correlation of FM_index for some k

Baker's Gamma correlation coefficient

Proportion of commong nodes between two trees

Cophenetic correlation between two trees

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

Cut a dendrogram - and run a function on the output

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

cutree for dendrogram (by 1 height only!)

cutree for dendrogram (by 1 k value only!)

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

Functions for extending dendrogram objects

Access to dendextend_options

Creating a dendlist object from several dendrograms

Find minimum/maximum depth of a dendrogram

Topological Distances Between Two dendrograms

Turns a dist object to a "long" table

Finds distinct edges in one tree compared to another

Duplicate a leaf X times

Measures entanglement between two trees

Turns a factor into a number

Finds a "good" dendrogram for a dist

Search for the sub-dendrogram structure composed of selected labels

Find the (estimated) number of clusters for a dendrogram using average silhouette width

Fix members attr in a dendrogram

Flatten the branches of a dendrogram's root

Flip leaves

Get height attributes from a dendrogram

Get height attributes from a dendrogram's children

Get/set attributes of dendrogram's leaves

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

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

Get edgePar of dendrogram's leaves

Get nodePar of dendrogram's leaves

Get attributes of dendrogram's nodes

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

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

Extract a list of k subdendrograms from a given dendrogram object

Creates dendrogram plot using ggplot.

Hang dendrogram leaves

Does a dendrogram has an edgePar/nodePar component?

Which height will result in which k for a dendrogram

Highlight a dendrogram's branches heights via color and line-width

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

Identify Clusters in a Dendrogram (not hclust)

Intersect trees

Check if numbers are natural

Checks if the value is and empty list()

Is the object of some class

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

"label" assignment operator

Retrieve/assign cex to the labels of a dendrogram

Retrieve/assign colors to the labels of a dendrogram

Ladderize a Tree

Return the leaf Colors of a dendrogram

Find lowest common branch were the two items are shared

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

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

Last Observation Carried Forward

Counts the number of leaves in a tree

Counts the number of nodes (Vertices) in a tree

Find which nodes satisfies a condition

order.dendrogram<- assignment operator

Ordering of the Leaves in a hclust Dendrogram

A list with labels for each subtree (edge)

Plotting a left-tip-adjusted horizontal dendrogram

Prunes a tree (using leaves' labels)

Prune trees to their common subtrees

Trims one leaf from a dendrogram

Get Pvclust Edges Information

The significant branches in a dendrogram, based on a pvclust object

Significance gradient of branches in a dendrogram (via pvclust)

Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values

Raise the height of a dendrogram tree

Rank branches' heights

Fix rank of leaves order values in a dendrogram

Rank a vector based on clusters

Draw Rectangles Around a Dendrogram's Clusters

Objects exported from other packages

Reindexing a pruned dendrogram

Remove all edgePar values from a dendrogram's branches

Remove all nodePar values from a dendrogram's leaves

Remove all nodePar values from a dendrogram's nodes

recursivly apply a function on a list

Rotate a tree object

Rotates dend based on DendSer

Sample a tree

Rotates a dendrogram based on a seriation of a distance matrix

Set (/update) features to a dendrogram

Set/place new labels in a dendrogram

Random rotation of trees

Sorts two clusters vector by their names

Sorts a distance matrix by rows and columns names

Sort the values level in a vector

Tanglegram plot

Creates completely blank theme in ggplot

unbranch trees

unclass an entire dendrogram tree

untangle dendrograms

Tries to run DendSer on a dendrogram

Untangle - random search

Stepwise untangle one tree compared to another

Stepwise untangle two trees one at a time

Which node is a leaf?

Which node id is common to a group of labels