Extending R's dendrogram functionality


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Documentation for package ‘dendextend’ version 0.12.2

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

dendextend-package Functions for extending dendrogram objsects

-- A --

all_couple_rotations_at_k Rotate tree branches for k
assign_values_to_branches_edgePar Assign values to edgePar of dendrogram's branches
assign_values_to_leaves_nodePar Assign values to nodePar of dendrogram's leaves
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

-- C --

color_branches Color tree's branches according to sub-clusters
color_labels Color tree's labels according to sub-clusters
colour_branches Color tree's branches according to sub-clusters
colour_labels Color tree's labels according to sub-clusters
cor_bakers_gamma Baker's Gamma correlation coefficient
cor_cophenetic Cophenetic correlation between two trees
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 --

dendbackback Tanglegram plot
dendextend Functions for extending dendrogram objsects
duplicate_leaf Duplicate a leaf X times

-- E --

entanglement Measures entanglement between two trees
entanglement.default 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
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_attr get attributes from the dendrogram's root branches
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_nodes_attr Get attributes of dendrogram's nodes

-- H --

hang.dendrogram Hang dendrogram leaves
heights_per_k.dendrogram Which height will result in which k for a dendrogram

-- I --

intersect_trees Intersect trees
is.dendrogram Is the object of class dendrogram
is.hclust Is the object of class hclust
is.natural.number Check if numbers are natural
is.phylo Is the object of class phylo

-- L --

labels.hclust "label" assignment operator
labels.matrix "label" assignment operator
labels<- "label" assignment operator
labels<-.default "label" assignment operator
labels<-.dendrogram "label" assignment operator
labels<-.hclust "label" assignment operator
labels<-.matrix "label" assignment operator
labels_colors Retrieve/assign colors to the labels of a dendrogram
labels_colors<- Retrieve/assign colors to the labels of a dendrogram
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 --

nleaves Counts the number of leaves in a tree
nleaves.default 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

-- O --

order.dendrogram<- order.dendrogram<- assignment operator

-- P --

plot_horiz.dendrogram Plotting a left-tip-adjusted horizontal dendrogram
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_leaf Trimms one leaf from a dendrogram

-- 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
remove_branches_edgePar Remove all edgePar values from a dendrogram's branches
remove_leaves_nodePar Remove all nodePar values from a dendrogram's leaves
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

-- S --

sample.dendrogram Sample a tree
shuffle Random rotation of trees
shuffle.default Random rotation of trees
shuffle.dendrogram Random rotation of trees
shuffle.hclust Random rotation of trees
shuffle.phylo Random rotation of trees
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
sort_levels_values Sort the values level in a vector

-- T --

tanglegram Tanglegram plot
tanglegram.default Tanglegram plot
tanglegram.dendrogram Tanglegram plot
tanglegram.hclust Tanglegram plot
tanglegram.phylo Tanglegram plot

-- 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_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