dendextend: Extending R's Dendrogram Functionality

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Offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.

Author
Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Yoav Benjamini [ths]
Date of publication
2016-08-27 14:17:20
Maintainer
Tal Galili <tal.galili@gmail.com>
License
GPL-2 | GPL-3
Version
1.3.0
URLs

View on CRAN

Man pages

all_couple_rotations_at_k
Rotate tree branches for k
all.equal.dendrogram
Global Comparison of two (or more) dendrograms
all_unique
Check if all the elements in a vector are unique
as.dendlist
Try to coerce something into a dendlist
as_hclust_fixed
Convert dendrogram Objects to Class hclust
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
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...
Bk_plot
Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram...
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
circlize_dendrogram
Plot a circlized dendrograms
click_rotate
Interactively rotate a tree object
collapse_branch
Collapse branches under a tolerance level
color_branches
Color tree's branches according to sub-clusters
colored_bars
Add colored bars to a dendrogram
color_labels
Color dend's labels according to sub-clusters
color_unique_labels
Color unique labels in a dendrogram
common_subtrees_clusters
Find clusters of common subtrees
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
cor.dendlist
Correlation matrix between a list of trees.
cor_FM_index
Correlation of FM_index for some k
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_1h.dendrogram
cutree for dendrogram (by 1 height only!)
cutree_1k.dendrogram
cutree for dendrogram (by 1 k value only!)
cutree-methods
Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
d3dendrogram
Plot dendrogram to webpage and view.
d3dendro_options
Get or set current defaults for d3dendrogram
dend_diff
Plots two trees side by side, highlighting edges unique to...
dendextend_labels.dendrogram
Labels of the Leaves in a Dendrogram
dendextend_options
Access to dendextend_options
dendextend-package
Functions for extending dendrogram objects
dendlist
Creating a dendlist object from several dendrograms
DendSer.dendrogram
Tries to run DendSer on a dendrogram
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
entanglement
Measures entanglement between two trees
fac2num
Turns a factor into a number
find_k
Find the (estimated) number of clusters for a dendrogram...
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
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.
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)
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_null_list
Checks if the value is and empty list()
is.phylo
Is the object of class phylo
khan
Microarray gene expression dataset from Khan et al., 2001....
labels-assign
"label" assignment operator
labels_cex
Retrieve/assign cex to the labels of a dendrogram
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...
match_order_dendrogram_by_old_order
Adjust the order of one dendrogram based on another (using...
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-assign
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_show_signif
The significant branches in a dendrogram, based on a pvclust...
pvclust_show_signif_gradient
Significance gradient of branches in a dendrogram (via...
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
reexports
Objects exported from other packages
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
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...
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
Tanglegram plot
theme_dendro
Creates completely blank theme in ggplot
unbranch
unbranch trees
unclass_dend
unclass an entire dendrogram tree
untangle
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
which_leaf
Which node is a leaf?
which_node
Which node id is common to a group of labels

Files in this package

dendextend
dendextend/TODO
dendextend/inst
dendextend/inst/CITATION
dendextend/inst/doc
dendextend/inst/doc/FAQ.Rmd
dendextend/inst/doc/Cluster_Analysis.html
dendextend/inst/doc/FAQ.html
dendextend/inst/doc/Cluster_Analysis.R
dendextend/inst/doc/Quick_Introduction.Rmd
dendextend/inst/doc/Quick_Introduction.html
dendextend/inst/doc/Cluster_Analysis.Rmd
dendextend/inst/doc/introduction.R
dendextend/inst/doc/introduction.html
dendextend/inst/doc/Quick_Introduction.R
dendextend/inst/doc/introduction.Rmd
dendextend/inst/doc/FAQ.R
dendextend/tests
dendextend/tests/testthat
dendextend/tests/testthat/test-entanglement.R
dendextend/tests/testthat/test-dendlist.R
dendextend/tests/testthat/test-cor_bakers_gamma.R
dendextend/tests/testthat/test-rotate.R
dendextend/tests/testthat/test-bk_method.R
dendextend/tests/testthat/test-attr_access.R
dendextend/tests/testthat/test-ggdend.R
dendextend/tests/testthat/test-cutree.dendrogram.R
dendextend/tests/testthat/test-set.dendrogram.R
dendextend/tests/testthat/test-cut_lower_fun.R
dendextend/tests/testthat/test-trim.R
dendextend/tests/testthat/test-untangle.R
dendextend/tests/testthat/test-rect.dendrogram.R
dendextend/tests/testthat/test-labels_colors.R
dendextend/tests/testthat/test-distinct_edges.R
dendextend/tests/testthat/test-nleaves.R
dendextend/tests/testthat/test-general.R
dendextend/tests/testthat/test-unbranch.R
dendextend/tests/testthat/test-labels-assign.R
dendextend/tests/testthat/test-common_subtrees.R
dendextend/tests/testthat/test-branches_attr_by.R
dendextend/tests/testthat/test-cor_cophenetic.R
dendextend/tests/test-all.R
dendextend/NAMESPACE
dendextend/demo
dendextend/demo/dendextend.R
dendextend/demo/00Index
dendextend/NEWS
dendextend/NEWS.md
dendextend/data
dendextend/data/khan.rda
dendextend/R
dendextend/R/pvclust.R
dendextend/R/cut_lower_fun.R
dendextend/R/rect.dendrogram.R
dendextend/R/attr_access.R
dendextend/R/cutree.dendrogram.R
dendextend/R/dendextend-package.R
dendextend/R/is.functions.R
dendextend/R/noded_with_condition.R
dendextend/R/nleaves.R
dendextend/R/d3dendrogram.R
dendextend/R/DendSer.R
dendextend/R/all.equal.R
dendextend/R/cor_bakers_gamma.R
dendextend/R/ggdend.R
dendextend/R/colored_bars.R
dendextend/R/circlize.R
dendextend/R/labels_colors.R
dendextend/R/sample.dendrogram.R
dendextend/R/cor_cophenetic.R
dendextend/R/seriate_dendrogram.R
dendextend/R/dendlist.R
dendextend/R/magrittr.R
dendextend/R/common_subtrees.R
dendextend/R/entanglement.R
dendextend/R/data.R
dendextend/R/stats_imports.R
dendextend/R/rotate.R
dendextend/R/dist_long.R
dendextend/R/distinct_edges.R
dendextend/R/ggdendro.R
dendextend/R/dendextend.R
dendextend/R/tanglegram.R
dendextend/R/set.dendrogram.R
dendextend/R/bk_method.R
dendextend/R/color_branches.R
dendextend/R/ape.R
dendextend/R/untangle.R
dendextend/R/as.dendrogram.randomForest.R
dendextend/R/branches_attr_by.R
dendextend/R/unbranch.R
dendextend/R/labels.R
dendextend/R/cor.dendlist.R
dendextend/R/get_nodes_xy.R
dendextend/R/rainbow_fun.R
dendextend/R/prune.R
dendextend/R/dendextend_options.R
dendextend/R/zzz.R
dendextend/R/find_k.R
dendextend/vignettes
dendextend/vignettes/FAQ.Rmd
dendextend/vignettes/Quick_Introduction.Rmd
dendextend/vignettes/Cluster_Analysis.Rmd
dendextend/vignettes/disabled
dendextend/vignettes/disabled/dendextend-tutorial.rnw
dendextend/vignettes/introduction.Rmd
dendextend/README.md
dendextend/MD5
dendextend/build
dendextend/build/vignette.rds
dendextend/DESCRIPTION
dendextend/ChangeLog
dendextend/man
dendextend/man/remove_leaves_nodePar.Rd
dendextend/man/remove_branches_edgePar.Rd
dendextend/man/rank_order.dendrogram.Rd
dendextend/man/labels_colors.Rd
dendextend/man/dist.dendlist.Rd
dendextend/man/get_root_branches_attr.Rd
dendextend/man/set.Rd
dendextend/man/rllply.Rd
dendextend/man/sample.dendrogram.Rd
dendextend/man/dist_long.Rd
dendextend/man/highlight_distinct_edges.Rd
dendextend/man/cor_common_nodes.Rd
dendextend/man/pvclust_show_signif.Rd
dendextend/man/nleaves.Rd
dendextend/man/tanglegram.Rd
dendextend/man/as.phylo.dendrogram.Rd
dendextend/man/order.hclust.Rd
dendextend/man/partition_leaves.Rd
dendextend/man/get_childrens_heights.Rd
dendextend/man/hang.dendrogram.Rd
dendextend/man/which_leaf.Rd
dendextend/man/FM_index_permutation.Rd
dendextend/man/d3dendrogram.Rd
dendextend/man/is.dendlist.Rd
dendextend/man/color_unique_labels.Rd
dendextend/man/is.hclust.Rd
dendextend/man/labels-assign.Rd
dendextend/man/leaf_Colors.Rd
dendextend/man/get_nodes_xy.Rd
dendextend/man/click_rotate.Rd
dendextend/man/assign_values_to_branches_edgePar.Rd
dendextend/man/is.natural.number.Rd
dendextend/man/theme_dendro.Rd
dendextend/man/seriate_dendrogram.Rd
dendextend/man/fix_members_attr.dendrogram.Rd
dendextend/man/ggdend.Rd
dendextend/man/khan.Rd
dendextend/man/fac2num.Rd
dendextend/man/raise.dendrogram.Rd
dendextend/man/prune_common_subtrees.dendlist.Rd
dendextend/man/dendlist.Rd
dendextend/man/distinct_edges.Rd
dendextend/man/color_branches.Rd
dendextend/man/assign_values_to_nodes_nodePar.Rd
dendextend/man/flatten.dendrogram.Rd
dendextend/man/get_nodes_attr.Rd
dendextend/man/rank_values_with_clusters.Rd
dendextend/man/sort_2_clusters_vectors.Rd
dendextend/man/rotate.Rd
dendextend/man/heights_per_k.dendrogram.Rd
dendextend/man/all_couple_rotations_at_k.Rd
dendextend/man/flip_leaves.Rd
dendextend/man/rank_branches.Rd
dendextend/man/which_node.Rd
dendextend/man/FM_index_profdpm.Rd
dendextend/man/cor_bakers_gamma.Rd
dendextend/man/identify.dendrogram.Rd
dendextend/man/all.equal.dendrogram.Rd
dendextend/man/assign_dendextend_options.Rd
dendextend/man/is.dendrogram.Rd
dendextend/man/untangle_random_search.Rd
dendextend/man/untangle_step_rotate_1side.Rd
dendextend/man/dendextend-package.Rd
dendextend/man/unbranch.Rd
dendextend/man/pvclust_show_signif_gradient.Rd
dendextend/man/cutree_1k.dendrogram.Rd
dendextend/man/match_order_dendrogram_by_old_order.Rd
dendextend/man/intersect_trees.Rd
dendextend/man/cutree_1h.dendrogram.Rd
dendextend/man/prune.Rd
dendextend/man/color_labels.Rd
dendextend/man/DendSer.dendrogram.Rd
dendextend/man/Bk_plot.Rd
dendextend/man/circlize_dendrogram.Rd
dendextend/man/duplicate_leaf.Rd
dendextend/man/dendextend_labels.dendrogram.Rd
dendextend/man/get_branches_heights.Rd
dendextend/man/rect.dendrogram.Rd
dendextend/man/untangle.Rd
dendextend/man/reexports.Rd
dendextend/man/remove_nodes_nodePar.Rd
dendextend/man/as.dendlist.Rd
dendextend/man/prune_leaf.Rd
dendextend/man/get_leaves_branches_attr.Rd
dendextend/man/rotate_DendSer.Rd
dendextend/man/cor_FM_index.Rd
dendextend/man/Bk.Rd
dendextend/man/cutree-methods.Rd
dendextend/man/cor_cophenetic.Rd
dendextend/man/get_leaves_attr.Rd
dendextend/man/count_terminal_nodes.Rd
dendextend/man/as_hclust_fixed.Rd
dendextend/man/sort_levels_values.Rd
dendextend/man/untangle_DendSer.Rd
dendextend/man/branches_attr_by_labels.Rd
dendextend/man/entanglement.Rd
dendextend/man/sort_dist_mat.Rd
dendextend/man/get_leaves_nodePar.Rd
dendextend/man/match_order_by_labels.Rd
dendextend/man/plot_horiz.dendrogram.Rd
dendextend/man/unclass_dend.Rd
dendextend/man/FM_index.Rd
dendextend/man/untangle_step_rotate_2side.Rd
dendextend/man/noded_with_condition.Rd
dendextend/man/d3dendro_options.Rd
dendextend/man/dend_diff.Rd
dendextend/man/all_unique.Rd
dendextend/man/order.dendrogram-assign.Rd
dendextend/man/is.phylo.Rd
dendextend/man/na_locf.Rd
dendextend/man/assign_values_to_leaves_edgePar.Rd
dendextend/man/assign_values_to_leaves_nodePar.Rd
dendextend/man/dendextend_options.Rd
dendextend/man/Bk_permutations.Rd
dendextend/man/nnodes.Rd
dendextend/man/colored_bars.Rd
dendextend/man/is_null_list.Rd
dendextend/man/labels_cex.Rd
dendextend/man/get_leaves_branches_col.Rd
dendextend/man/ladderize.Rd
dendextend/man/cut_lower_fun.Rd
dendextend/man/find_k.Rd
dendextend/man/collapse_branch.Rd
dendextend/man/FM_index_R.Rd
dendextend/man/get_leaves_edgePar.Rd
dendextend/man/lowest_common_branch.Rd
dendextend/man/cor.dendlist.Rd
dendextend/man/common_subtrees_clusters.Rd
dendextend/man/is.dist.Rd
dendextend/man/bakers_gamma_for_2_k_matrix.Rd
dendextend/man/shuffle.Rd
dendextend/man/branches_attr_by_clusters.Rd
dendextend/man/set_labels.Rd