dendextend: Extending 'Dendrogram' Functionality in R

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.

AuthorTal Galili [aut, cre, cph] (https://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), Cath [ctb] (https://github.com/CathG), Yoav Benjamini [ths]
Date of publication2017-01-21 23:17:20
MaintainerTal Galili <tal.galili@gmail.com>
LicenseGPL-2 | GPL-3
Version1.4.0
https://cran.r-project.org/package=dendextend, https://github.com/talgalili/dendextend/, https://www.r-statistics.com/tag/dendextend/, https://bioinformatics.oxfordjournals.org/content/31/22/3718

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

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: Highlight a dendrogram's branches heights via color and...

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/highlight_branches.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/Hmisc.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/has_edgePar.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/highlight_branches.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/has_component_in_attribute.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

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