dendextend: Extending R's Dendrogram Functionality

樹形図描画の拡張

> library(dendextend)


Welcome to dendextend version 1.1.8

Type ?dendextend to access the overall documentation and
browseVignettes(package = 'dendextend') for the package vignette.
You can execute a demo of the package via: demo(dendextend)

More information is available on the dendextend project web-site:
https://github.com/talgalili/dendextend/

Contact: <tal.galili@gmail.com>
Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues

            To suppress this message use:
            suppressPackageStartupMessages(library(dendextend))


Attaching package: 'dendextend'

The following object is masked from 'package:webshot':

    %>%

The following object is masked from 'package:stats':

    cutree

The following object is masked from 'package:magrittr':

    %>%

バージョン: 1.1.8

.
%>% Pipe an object forward into a function
call/expression.
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
DendSer.dendrogram Tries to run DendSer on a dendrogram
FM_index Calculating Fowlkes-Mallows Index
FM_index_R Calculating Fowlkes-Mallows index in R
FM_index_permutation Calculating Fowlkes-Mallows Index under H0
FM_index_profdpm Calculating Fowlkes-Mallows index using the
profdpm R package
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.phylo.dendrogram Convert a dendrogram into phylo
as_hclust_fixed Convert dendrogram Objects to Class hclust
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
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
color_labels Color dend's labels according to sub-clusters
color_unique_labels Color unique labels in a dendrogram
colored_bars Add colored bars to a dendrogram
common_subtrees_clusters
Find clusters of common subtrees
cor.dendlist Correlation matrix between a list of trees.
cor_FM_index Correlation of FM_index for some k
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
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 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!)
d3dendro_options Get or set current defaults for d3dendrogram
d3dendrogram Plot dendrogram to webpage and view.
dend_diff Plots two trees side by side, highlighting
edges unique to each tree in red.
dendextend-package Functions for extending dendrogram objects
dendextend_labels.dendrogram
Labels of the Leaves in a Dendrogram
dendextend_options Access to dendextend_options
dendlist Creating a dendlist object from several
dendrograms
dist.dendlist Topological Distances Between Two dendrograms
dist_long Turns a dist object to a "long" table
distinct_edges Finds distinct edges in one tree compared to
another
duplicate_leaf Duplicate a leaf X times
entanglement Measures entanglement between two trees
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
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.hclust Is the object of class hclust
is.natural.number Check if numbers are natural
is.phylo Is the object of class phylo
is_null_list Checks if the value is and empty list()
khan Microarray gene expression dataset from Khan et
al., 2001. Subset of 306 genes.
labels<- "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 labels)
match_order_dendrogram_by_old_order
Adjust the order of one dendrogram based on
another (using order)
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<- 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 object
pvclust_show_signif_gradient
Significance gradient of branches in a
dendrogram (via pvclust)
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
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
set Set (/update) features to 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
関数名 概略
%>% Pipe an object forward into a function call/expression.
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
DendSer.dendrogram Tries to run DendSer on a dendrogram
FM_index Calculating Fowlkes-Mallows Index
FM_index_R Calculating Fowlkes-Mallows index in R
FM_index_permutation Calculating Fowlkes-Mallows Index under H0
FM_index_profdpm Calculating Fowlkes-Mallows index using the profdpm R package
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.phylo.dendrogram Convert a dendrogram into phylo
as_hclust_fixed Convert dendrogram Objects to Class hclust
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
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
color_labels Color dend's labels according to sub-clusters
color_unique_labels Color unique labels in a dendrogram
colored_bars Add colored bars to a dendrogram
common_subtrees_clusters Find clusters of common subtrees
cor.dendlist Correlation matrix between a list of trees.
cor_FM_index Correlation of FM_index for some k
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
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 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!)
d3dendro_options Get or set current defaults for d3dendrogram
d3dendrogram Plot dendrogram to webpage and view.
dend_diff Plots two trees side by side, highlighting edges unique to each tree in red.
dendextend-package Functions for extending dendrogram objects
dendextend_labels.dendrogram Labels of the Leaves in a Dendrogram
dendextend_options Access to dendextend_options
dendlist Creating a dendlist object from several dendrograms
dist.dendlist Topological Distances Between Two dendrograms
dist_long Turns a dist object to a "long" table
distinct_edges Finds distinct edges in one tree compared to another
duplicate_leaf Duplicate a leaf X times
entanglement Measures entanglement between two trees
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
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.hclust Is the object of class hclust
is.natural.number Check if numbers are natural
is.phylo Is the object of class phylo
is_null_list Checks if the value is and empty list()
khan Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
labels<- "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 labels)
match_order_dendrogram_by_old_order Adjust the order of one dendrogram based on another (using order)
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<- 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 object
pvclust_show_signif_gradient Significance gradient of branches in a dendrogram (via pvclust)
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
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
set Set (/update) features to 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