Extending 'dendrogram' Functionality in R


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Documentation for package ‘dendextend’ version 1.15.1

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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_attr_by_lists Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members
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
colored_dots Add colored dots beside 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.default 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.agnes 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.diana 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 objects
dendextend_cut_lower_fun Cut a dendrogram - and run a function on the output
dendextend_heights_per_k.dendrogram Which height will result in which k for 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.
dend_expend Finds a "good" dendrogram for a dist
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.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_dend Finds a "good" dendrogram for a dist
find_dendrogram Search for the sub-dendrogram structure composed of selected labels
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_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
get_subdendrograms Extract a list of _k_ subdendrograms from a given dendrogram object
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
has_component_in_attribute Does a dendrogram has an edgePar/nodePar component?
has_edgePar Does a dendrogram has an edgePar/nodePar component?
has_nodePar Does a dendrogram has an edgePar/nodePar component?
heights_per_k.dendrogram Which height will result in which k for a dendrogram
highlight_branches Highlight a dendrogram's branches heights via color and line-width
highlight_branches_col Highlight a dendrogram's branches heights via color and line-width
highlight_branches_lwd Highlight a dendrogram's branches heights via color and line-width
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 Is the object of some class
is.dendrogram Is the object of some class
is.dist Is the object of some class
is.hclust Is the object of some class
is.natural.number Check if numbers are natural
is.phylo Is the object of some class
is_null_list Checks if the value is and empty list()
is_some_class Is the object of some class

-- 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)
max_depth Find minimum/maximum depth of a dendrogram
min_depth Find minimum/maximum depth of a dendrogram

-- 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.
print.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_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

-- 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
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
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_labels untangle dendrograms
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