Package index • dendextend

All functions
`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
`DendSer.dendrogram()`	Tries to run DendSer on a dendrogram
`FM_index()`	Calculating Fowlkes-Mallows Index
`FM_index_R()`	Calculating Fowlkes-Mallows index in R
`FM_index_permutation()`	Calculating Fowlkes-Mallows Index under H0
`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.phylo.dendrogram()`	Convert a dendrogram into phylo
`as_hclust_fixed()`	Convert dendrogram Objects to Class hclust
`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
`bakers_gamma_for_2_k_matrix()`	Bakers Gamma for two k matrices
`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_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
`click_rotate()`	Interactively rotate a tree object
`collapse_branch()`	Collapse branches under a tolerance level
`collapse_labels()`	Collapse a sub dendrogram of adjacent labels within a dend
`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
`colored_bars()`	Add colored bars to a dendrogram
`colored_dots()`	Add colored dots beside a dendrogram
`common_subtrees_clusters()`	Find clusters of common subtrees
`cor.dendlist()`	Correlation matrix between a list of trees.
`cor_FM_index()`	Correlation of FM_index for some k
`cor_bakers_gamma()`	Baker's Gamma correlation coefficient
`cor_common_nodes()`	Proportion of commong nodes between two trees
`cor_cophenetic()`	Cophenetic correlation between two trees
`count_terminal_nodes()`	Counts the number of terminal nodes (merging 0 nodes!)
`cut_lower_fun()`	Cut a dendrogram - and run a function on the output
`cutree()`	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!)
`dend_diff()`	Plots two trees side by side, highlighting edges unique to each tree in red.
`dendextend-package` `dendextend`	Functions for extending dendrogram objects
`dendextend_options()`	Access to dendextend_options
`dendlist()` `plot(<dendlist>)`	Creating a dendlist object from several dendrograms
`min_depth()` `max_depth()`	Find minimum/maximum depth of a dendrogram
`dist.dendlist()`	Topological Distances Between Two dendrograms
`dist_long()`	Turns a dist object to a "long" table
`distinct_edges()`	Finds distinct edges in one tree compared to another
`duplicate_leaf()`	Duplicate a leaf X times
`entanglement()`	Measures entanglement between two trees
`fac2num()`	Turns a factor into a number
`dend_expend()` `find_dend()`	Finds a "good" dendrogram for a dist
`find_dendrogram()`	Search for the sub-dendrogram structure composed of selected labels
`find_k()` `plot(<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
`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
`get_subdendrograms()`	Extract a list of k subdendrograms from a given dendrogram object
`ggdend()` `as.ggdend()` `prepare.ggdend()` `ggplot(<ggdend>)` `ggplot(<dendrogram>)` `print(<ggdend>)`	Creates dendrogram plot using ggplot.
`hang.dendrogram()`	Hang dendrogram leaves
`has_component_in_attribute()`	Does a dendrogram has an edgePar/nodePar component?
`heights_per_k.dendrogram()`	Which height will result in which k for a dendrogram
`highlight_branches_col()` `highlight_branches_lwd()` `highlight_branches()`	Highlight a dendrogram's branches heights via color and line-width
`highlight_distinct_edges()`	Highlight distint edges in a tree (compared to another one)
`identify(<dendrogram>)`	Identify Clusters in a Dendrogram (not hclust)
`intersect_trees()`	Intersect trees
`is.natural.number()`	Check if numbers are natural
`is_null_list()`	Checks if the value is and empty list()
`is.hclust()` `is.dendrogram()` `is.phylo()` `is.dendlist()` `is.dist()`	Is the object of some class
`khan`	Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
`labels<-`() `labels(<hclust>)` `labels(<phylo>)`	"label" assignment operator
`labels_cex()` `labels_cex<-`()	Retrieve/assign cex to the labels of a dendrogram
`labels_colors()` `labels_col()` `labels_colors<-`()	Retrieve/assign colors to the labels of a dendrogram
`ladderize()`	Ladderize a Tree
`leaf_Colors()`	Return the leaf Colors of a dendrogram
`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)
`match_order_dendrogram_by_old_order()`	Adjust the order of one dendrogram based on another (using order)
`na_locf()`	Last Observation Carried Forward
`nleaves()`	Counts the number of leaves in a tree
`nnodes()`	Counts the number of nodes (Vertices) in a tree
`noded_with_condition()`	Find which nodes satisfies a condition
`order.dendrogram<-`()	order.dendrogram<- assignment operator
`order.hclust()`	Ordering of the Leaves in a hclust Dendrogram
`partition_leaves()`	A list with labels for each subtree (edge)
`plot_horiz.dendrogram()`	Plotting a left-tip-adjusted horizontal dendrogram
`prune()`	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_edges()`	Get Pvclust Edges Information
`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)
`pvrect2()`	Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values
`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
`reindex_dend()`	Reindexing a pruned 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
`remove_nodes_nodePar()`	Remove all nodePar values from a dendrogram's nodes
`rllply()`	recursivly apply a function on a list
`rotate()` `sort(<dendrogram>)` `sort(<hclust>)` `sort(<dendlist>)` `rev(<hclust>)`	Rotate a tree object
`rotate_DendSer()`	Rotates dend based on DendSer
`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_labels()`	Set/place new labels in a dendrogram
`shuffle()`	Random rotation of trees
`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
`tanglegram()` `dendbackback()`	Tanglegram plot
`theme_dendro()`	Creates completely blank theme in ggplot
`unbranch()`	unbranch trees
`unclass_dend()`	unclass an entire dendrogram tree
`untangle()` `untangle_labels()`	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
`untangle_step_rotate_both_side()`	Stepwise untangle two trees at the same time
`which_leaf()`	Which node is a leaf?
`which_node()`	Which node id is common to a group of labels

Reference

All functions