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dendextend (version 0.14.2)
Extending R's dendrogram functionality
Description
Functions and methods for extending dendrogram objects in R.
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Install
install.packages('dendextend')
Monthly Downloads
68,312
Version
0.14.2
License
GPL-2 | GPL-3
Issues
56
Pull Requests
0
Stars
148
Forks
28
Repository
https://github.com/talgalili/dendextend/
Homepage
http://www.r-statistics.com/tag/dendextend/
Maintainer
Tal Galili
Last Published
March 15th, 2014
Functions in dendextend (0.14.2)
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lowest_common_branch
Find lowest common branch were the two items are shared
FM_index_permutation
Calculating Fowlkes-Mallows Index under H0
is.natural.number
Check if numbers are natural
color_branches
Color tree's branches according to sub-clusters
get_nodes_attr
Get attributes of dendrogram's nodes
count_terminal_nodes
Counts the number of terminal nodes (merging 0 nodes!)
assign_values_to_leaves_nodePar
Assign values to nodePar of dendrogram's leaves
nleaves
Counts the number of leaves in a tree
raise.dendrogram
Raise the height of a dendrogram tree
assign_dendextend_options
Populates dendextend functions into dendextend_options
prune_leaf
Trimms one leaf from a dendrogram
fac2num
Turns a factor into a number
labels_colors
Retrieve/assign colors to the labels of a dendrogram
get_branches_heights
Get height attributes from a dendrogram
Bk_plot
Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's
remove_branches_edgePar
Remove all edgePar values from a dendrogram's branches
remove_leaves_nodePar
Remove all nodePar values from a dendrogram's leaves
sample.dendrogram
Sample a tree
get_branches_attr
get attributes from the dendrogram's root branches
untangle_step_rotate_1side
Stepwise untangle one tree compared to another
assign_values_to_branches_edgePar
Assign values to edgePar of dendrogram's branches
cutree_1h.dendrogram
cutree for dendrogram (by 1 height only!)
plot_horiz.dendrogram
Plotting a left-tip-adjusted horizontal dendrogram
is.hclust
Is the object of class hclust
match_order_by_labels
Adjust the order of one dendrogram based on another (using labels)
color_labels
Color tree's labels according to sub-clusters
leaf_Colors
Return the leaf Colors of a dendrogram
labels<-
"label" assignment operator
cut_lower_fun
Cut a dendrogram - and run a function on the output
Bk_permutations
Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram
is.dendrogram
Is the object of class dendrogram
flip_leaves
Flip leaves
get_leaves_attr
Get/set attributes of dendrogram's leaves
unclass_dend
unclass an entire dendrogram tree
FM_index_R
Calculating Fowlkes-Mallows index in R
bakers_gamma_for_2_k_matrix
Bakers Gamma for two k matrices
flatten.dendrogram
Flatten the branches of a dendrogram's root
is.phylo
Is the object of class phylo
dendextend-package
Functions for extending dendrogram objects
fix_members_attr.dendrogram
Fix members attr in a dendrogram
sort_2_clusters_vectors
Sorts two clusters vector by their names
FM_index
Calculating Fowlkes-Mallows Index
FM_index_profdpm
Calculating Fowlkes-Mallows index using the profdpm R package
all_couple_rotations_at_k
Rotate tree branches for k
as_hclust_fixed
Convert dendrogram Objects to Class hclust
cor_cophenetic
Cophenetic correlation between two trees
Bk
Bk - Calculating Fowlkes-Mallows Index for two dendrogram
heights_per_k.dendrogram
Which height will result in which k for a dendrogram
tanglegram
Tanglegram plot
rank_order.dendrogram
Fix rank of leaves order values in a dendrogram
unbranch
unbranch trees
nnodes
Counts the number of nodes (Vertices) in a tree
rllply
recursivly apply a function on a list
rotate
Rotate a tree object
rank_branches
Rank branches' heights
sort_levels_values
Sort the values level in a vector
match_order_dendrogram_by_old_order
Adjust the order of one dendrogram based on another (using order)
entanglement
Measures entanglement between two trees
order.dendrogram<-
order.dendrogram<- assignment operator
shuffle
Random rotation of trees
sort_dist_mat
Sorts a distance matrix by rows and columns
untangle_random_search
Untangle - random search
cutree
Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
cutree_1k.dendrogram
cutree for dendrogram (by 1 k value only!)
dendextend_options
Access to dendextend_options
get_childrens_heights
Get height attributes from a dendrogram's children
cor_bakers_gamma
Baker's Gamma correlation coefficient
intersect_trees
Intersect trees
untangle_step_rotate_2side
Stepwise untangle two trees one at a time
duplicate_leaf
Duplicate a leaf X times
prune
Prunes a tree (using leaves' labels)
hang.dendrogram
Hang dendrogram leaves