# Extending R's Dendrogram Functionality

## Documentation for package ‘dendextend’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P R S T U W

dendextend-package | Functions for extending dendrogram objects

## -- A --

all.equal.dendlist | Global Comparison of two (or more) dendrograms
all.equal.dendrogram | Global Comparison of two (or more) dendrograms
all_couple_rotations_at_k | Rotate tree branches for k
all_unique | Check if all the elements in a vector are unique
as.dendlist | Try to coerce something into a dendlist
as.ggdend | Creates dendrogram plot using ggplot.
as.ggdend.dendrogram | Creates dendrogram plot using ggplot.
as.phylo.dendrogram | Convert a dendrogram into phylo
assign_dendextend_options | Populates dendextend functions into dendextend_options
assign_values_to_branches_edgePar | Assign values to edgePar of dendrogram's branches
assign_values_to_leaves_edgePar | Assign values to edgePar of dendrogram's leaves
assign_values_to_leaves_nodePar | Assign values to nodePar of dendrogram's leaves
assign_values_to_nodes_nodePar | Assign values to nodePar of dendrogram's nodes
as_hclust_fixed | Convert dendrogram Objects to Class hclust

## -- B --

bakers_gamma_for_2_k_matrix | Bakers Gamma for two k matrices
Bk | Bk - Calculating Fowlkes-Mallows Index for two dendrogram
Bk_permutations | Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram
Bk_plot | Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's
branches_attr_by_clusters | Change col/lwd/lty of branches based on clusters
branches_attr_by_labels | Change col/lwd/lty of branches matching labels condition
branches_color | Color tree's branches according to sub-clusters

## -- C --

circlize_dendrogram | Plot a circlized dendrograms
click_rotate | Interactively rotate a tree object
click_rotate.default | Interactively rotate a tree object
click_rotate.dendrogram | Interactively rotate a tree object
collapse_branch | Collapse branches under a tolerance level
colored_bars | Add colored bars to a dendrogram
color_branches | Color tree's branches according to sub-clusters
color_labels | Color dend's labels according to sub-clusters
color_unique_labels | Color unique labels in a dendrogram
colour_branches | Color tree's branches according to sub-clusters
colour_labels | Color dend's labels according to sub-clusters
common_subtrees_clusters | Find clusters of common subtrees
cor.dendlist | Correlation matrix between a list of trees.
cor_bakers_gamma | Baker's Gamma correlation coefficient
cor_bakers_gamma.dendlist | Baker's Gamma correlation coefficient
cor_bakers_gamma.dendrogram | Baker's Gamma correlation coefficient
cor_bakers_gamma.hclust | Baker's Gamma correlation coefficient
cor_common_nodes | Proportion of commong nodes between two trees
cor_cophenetic | Cophenetic correlation between two trees
cor_cophenetic.default | Cophenetic correlation between two trees
cor_cophenetic.dendlist | Cophenetic correlation between two trees
cor_FM_index | Correlation of FM_index for some k
count_terminal_nodes | Counts the number of terminal nodes (merging 0 nodes!)
cutree | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree.default | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree.dendrogram | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree.hclust | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree.phylo | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree_1h.dendrogram | cutree for dendrogram (by 1 height only!)
cutree_1k.dendrogram | cutree for dendrogram (by 1 k value only!)
cut_lower_fun | Cut a dendrogram - and run a function on the output

## -- D --

d3dendrogram | Plot dendrogram to webpage and view.
d3dendro_options | Get or set current defaults for d3dendrogram
dendbackback | Tanglegram plot
dendextend | Functions for extending dendrogram objects
dendextend_cut_lower_fun | Cut a dendrogram - and run a function on the output
dendextend_get_branches_heights | Get height attributes from a dendrogram
dendextend_heights_per_k.dendrogram | Which height will result in which k for a dendrogram
dendextend_labels.dendrogram | Labels of the Leaves in a Dendrogram
dendextend_options | Access to dendextend_options
dendlist | Creating a dendlist object from several dendrograms
DendSer.dendrogram | Tries to run DendSer on a dendrogram
dend_diff | Plots two trees side by side, highlighting edges unique to each tree in red.
dend_diff.dendlist | Plots two trees side by side, highlighting edges unique to each tree in red.
dend_diff.dendrogram | Plots two trees side by side, highlighting edges unique to each tree in red.
dist.dendlist | Topological Distances Between Two dendrograms
distinct_edges | Finds distinct edges in one tree compared to another
dist_long | Turns a dist object to a "long" table
duplicate_leaf | Duplicate a leaf X times

## -- E --

entanglement | Measures entanglement between two trees
entanglement.default | Measures entanglement between two trees
entanglement.dendlist | Measures entanglement between two trees
entanglement.dendrogram | Measures entanglement between two trees
entanglement.hclust | Measures entanglement between two trees
entanglement.phylo | Measures entanglement between two trees

## -- F --

fac2num | Turns a factor into a number
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
flatten.dendrogram | Flatten the branches of a dendrogram's root
flip_leaves | Flip leaves
FM_index | Calculating Fowlkes-Mallows Index
FM_index_permutation | Calculating Fowlkes-Mallows Index under H0
FM_index_profdpm | Calculating Fowlkes-Mallows index using the profdpm R package
FM_index_R | Calculating Fowlkes-Mallows index in R

## -- G --

get_branches_heights | Get height attributes from a dendrogram
get_childrens_heights | Get height attributes from a dendrogram's children
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_leaves_branches_col | Get the colors of the branches of a dendrogram's leaves
get_leaves_edgePar | Get edgePar of dendrogram's leaves
get_leaves_nodePar | Get nodePar of dendrogram's leaves
get_nodes_attr | Get attributes of dendrogram's nodes
get_nodes_xy | Get the x-y coordinates of a dendrogram's nodes
get_root_branches_attr | get attributes from the dendrogram's root(!) branches
ggdend | Creates dendrogram plot using ggplot.
ggplot.dendrogram | Creates dendrogram plot using ggplot.
ggplot.ggdend | Creates dendrogram plot using ggplot.

## -- H --

hang.dendrogram | Hang dendrogram leaves
heights_per_k.dendrogram | Which height will result in which k for a dendrogram
highlight_distinct_edges | Highlight distint edges in a tree (compared to another one)
highlight_distinct_edges.dendlist | Highlight distint edges in a tree (compared to another one)
highlight_distinct_edges.dendrogram | Highlight distint edges in a tree (compared to another one)

## -- I --

identify.dendrogram | Identify Clusters in a Dendrogram (not hclust)
intersect_trees | Intersect trees
is.dendlist | Checks if an object is of class dendlist
is.dendrogram | Is the object of class dendrogram
is.dist | Checks if an object is of class dist
is.hclust | Is the object of class hclust
is.natural.number | Check if numbers are natural
is.phylo | Is the object of class phylo
is_null_list | Checks if the value is and empty list()

## -- K --

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

## -- L --

labels.hclust | "label" assignment operator
labels.phylo | "label" assignment operator
labels<- | "label" assignment operator
labels<-.default | "label" assignment operator
labels<-.dendrogram | "label" assignment operator
labels<-.hclust | "label" assignment operator
labels<-.phylo | "label" assignment operator
labels_cex | Retrieve/assign cex to the labels of a dendrogram
labels_cex<- | Retrieve/assign cex to the labels of a dendrogram
labels_col | Retrieve/assign colors to the labels of a dendrogram
labels_colors | Retrieve/assign colors to the labels of a dendrogram
labels_colors<- | Retrieve/assign colors to the labels of a dendrogram
ladderize | Ladderize a Tree
ladderize.dendlist | Ladderize a Tree
ladderize.dendrogram | Ladderize a Tree
ladderize.phylo | Ladderize a Tree
leaf_Colors | Return the leaf Colors of a dendrogram
leaf_colors | Return the leaf Colors of a dendrogram
lowest_common_branch | Find lowest common branch were the two items are shared

## -- M --

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

## -- N --

na_locf | Last Observation Carried Forward
nleaves | Counts the number of leaves in a tree
nleaves.default | Counts the number of leaves in a tree
nleaves.dendlist | Counts the number of leaves in a tree
nleaves.dendrogram | Counts the number of leaves in a tree
nleaves.hclust | Counts the number of leaves in a tree
nleaves.phylo | Counts the number of leaves in a tree
nnodes | Counts the number of nodes (Vertices) in a tree
nnodes.default | Counts the number of nodes (Vertices) in a tree
nnodes.dendrogram | Counts the number of nodes (Vertices) in a tree
nnodes.hclust | Counts the number of nodes (Vertices) in a tree
nnodes.phylo | Counts the number of nodes (Vertices) in a tree
noded_with_condition | Find which nodes satisfies a condition

## -- O --

order.dendrogram<- | order.dendrogram<- assignment operator
order.hclust | Ordering of the Leaves in a hclust Dendrogram

## -- P --

partition_leaves | A list with labels for each subtree (edge)
place_labels | Set/place new labels in a dendrogram
plot.dendlist | Creating a dendlist object from several dendrograms
plot.find_k | Find the (estimated) number of clusters for a dendrogram using average silhouette width
plot_horiz.dendrogram | Plotting a left-tip-adjusted horizontal dendrogram
prepare.ggdend | Creates dendrogram plot using ggplot.
prune | Prunes a tree (using leaves' labels)
prune.default | Prunes a tree (using leaves' labels)
prune.dendrogram | Prunes a tree (using leaves' labels)
prune.hclust | Prunes a tree (using leaves' labels)
prune.phylo | Prunes a tree (using leaves' labels)
prune.rpart | Prunes a tree (using leaves' labels)
prune_common_subtrees.dendlist | Prune trees to their common subtrees
prune_leaf | Trims one leaf from a dendrogram
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)

## -- R --

raise.dendrogram | Raise the height of a dendrogram tree
rank_branches | Rank branches' heights
rank_order.dendrogram | Fix rank of leaves order values in a dendrogram
rank_values_with_clusters | Rank a vector based on clusters
rect.dendrogram | Draw Rectangles Around a Dendrogram's Clusters
remove_branches_edgePar | Remove all edgePar values from a dendrogram's branches
remove_leaves_nodePar | Remove all nodePar values from a dendrogram's leaves
remove_nodes_nodePar | Remove all nodePar values from a dendrogram's nodes
rev.hclust | Rotate a tree object
rllply | recursivly apply a function on a list
rotate | Rotate a tree object
rotate.default | Rotate a tree object
rotate.dendrogram | Rotate a tree object
rotate.hclust | Rotate a tree object
rotate.phylo | Rotate a tree object
rotate_DendSer | Rotates dend based on DendSer

## -- S --

sample.dendrogram | Sample a tree
seriate_dendrogram | Rotates a dendrogram based on a seriation of a distance matrix
set | Set (/update) features to a dendrogram
set.data.table | Set (/update) features to a dendrogram
set.dendlist | Set (/update) features to a dendrogram
set.dendrogram | Set (/update) features to a dendrogram
set_labels | Set/place new labels in a dendrogram
shuffle | Random rotation of trees
shuffle.default | Random rotation of trees
shuffle.dendlist | Random rotation of trees
shuffle.dendrogram | Random rotation of trees
shuffle.hclust | Random rotation of trees
shuffle.phylo | Random rotation of trees
sort.dendlist | Rotate a tree object
sort.dendrogram | Rotate a tree object
sort.hclust | Rotate a tree object
sort_2_clusters_vectors | Sorts two clusters vector by their names
sort_dist_mat | Sorts a distance matrix by rows and columns names
sort_levels_values | Sort the values level in a vector

## -- T --

tanglegram | Tanglegram plot
tanglegram.default | Tanglegram plot
tanglegram.dendlist | Tanglegram plot
tanglegram.dendrogram | Tanglegram plot
tanglegram.hclust | Tanglegram plot
tanglegram.phylo | Tanglegram plot
theme_dendro | Creates completely blank theme in ggplot

## -- U --

unbranch | unbranch trees
unbranch.default | unbranch trees
unbranch.dendrogram | unbranch trees
unbranch.hclust | unbranch trees
unbranch.phylo | unbranch trees
unclass_dend | unclass an entire dendrogram tree
untangle | untangle dendrograms
untangle.default | untangle dendrograms
untangle.dendlist | untangle dendrograms
untangle.dendrogram | untangle dendrograms
untangle_DendSer | Tries to run DendSer on a dendrogram
untangle_random_search | Untangle - random search
untangle_step_rotate_1side | Stepwise untangle one tree compared to another
untangle_step_rotate_2side | Stepwise untangle two trees one at a time

## -- W --

which_leaf | Which node is a leaf?
which_node | Which node id is common to a group of labels