assign_values_to_leaves_edgePar
Assign values to edgePar of dendrogram's leaves
Correlation matrix between a list of trees.
assign_values_to_branches_edgePar
Assign values to edgePar of dendrogram's branches
assign_values_to_leaves_nodePar
Assign values to nodePar of dendrogram's leaves
Get/set attributes of dendrogram's leaves
Identify Clusters in a Dendrogram (not hclust)
Which height will result in which k for a dendrogram
Get the x-y coordiantes of a dendrogram's nodes
Shows the significant branches in a dendrogram, based on a pvclust object
Measures entanglement between two trees
bakers_gamma_for_2_k_matrix
Bakers Gamma for two k matrices
Calculating Fowlkes-Mallows index in R
Find lowest common branch were the two items are shared
Counts the number of terminal nodes (merging 0 nodes!)
Convert dendrogram Objects to Class hclust
Tanglegram plot
Turns a factor into a number
Functions for extending dendrogram objects
Creates dendrogram plot using ggplot.
Hang dendrogram leaves
rank_values_with_clusters
Rank a vector based on clusters
Retrieve/assign colors to the labels of a dendrogram
Sample a tree
Untangle - random search
Draw Rectangles Around a Dendrogram's Clusters
Remove all edgePar values from a dendrogram's branches
Calculating Fowlkes-Mallows Index
A list with labels for each subtree (edge)
Cophenetic correlation between two trees
Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram
Ladderize a Tree
Checks if an object is of class dendlist
untangle_step_rotate_1side
Stepwise untangle one tree compared to another
Plot dendrogram to webpage and view.
Change col/lwd/lty of branches matching labels condition
Intersect trees
Find which nodes satisfies a condition
Remove all nodePar values from a dendrogram's nodes
all_couple_rotations_at_k
Rotate tree branches for k
Get edgePar of dendrogram's leaves
Rotate a tree object
Set (/update) features to a dendrogram
unbranch trees
Check if numbers are natural
Sort the values level in a vector
Try to coerce something into a dendlist
Calculating Fowlkes-Mallows Index under H0
Color tree's branches according to sub-clusters
Pipe an object forward into a function call/expression.
Counts the number of leaves in a tree
Is the object of class dendrogram
Tries to run DendSer on a dendrogram
Baker's Gamma correlation coefficient
untangle dendrograms
Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
Cut a dendrogram - and run a function on the output
Checks if the value is and empty list()
Get an attribute of the branches of a dendrogram's leaves
Sorts two clusters vector by their names
Check if all the elements in a vector are unique
Get height attributes from a dendrogram
Ordering of the Leaves in a hclust Dendrogram
Last Observation Carried Forward
"label" assignment operator
Which node is a leaf?
Interactively rotate a tree object
Bk - Calculating Fowlkes-Mallows Index for two dendrogram
Correlation of FM_index for some k
assign_values_to_nodes_nodePar
Assign values to nodePar of dendrogram's nodes
Duplicate a leaf X times
Add colored bars to a dendrogram
Sorts a distance matrix by rows and columns
Flip leaves
Plotting a left-tip-adjusted horizontal dendrogram
Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
Get or set current defaults for d3dendrogram
Counts the number of nodes (Vertices) in a tree
cutree for dendrogram (by 1 k value only!)
untangle_step_rotate_2side
Stepwise untangle two trees one at a time
Rotates dend based on DendSer
fix_members_attr.dendrogram
Fix members attr in a dendrogram
Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's
Access to dendextend_options
Flatten the branches of a dendrogram's root
branches_attr_by_clusters
Change col/lwd/lty of branches based on clusters
assign_dendextend_options
Populates dendextend functions into dendextend_options
Proportion of commong nodes between two trees
Creating a dendlist object from several dendrograms
unclass an entire dendrogram tree
Find clusters of common subtrees
Random rotation of trees
Prunes a tree (using leaves' labels)
Get nodePar of dendrogram's leaves
Adjust the order of one dendrogram based on another (using labels)
dendextend_labels.dendrogram
Labels of the Leaves in a Dendrogram
Plots two trees side by side, highlighting edges unique to each tree in red.
Rank branches' heights
Which node id is common to a group of labels
Color dend's labels according to sub-clusters
Finds the edges present in the first tree but not in the second
Turns a dist object to a "long" table
Return the leaf Colors of a dendrogram
pvclust_show_signif_gradient
Shows the gradient of significance of branches in a dendrogram, based on a pvclust object
order.dendrogram<- assignment operator
cutree for dendrogram (by 1 height only!)
Collapse branches under a tolerance level
get attributes from the dendrogram's root(!) branches
Get height attributes from a dendrogram's children
Is the object of class phylo
Trimms one leaf from a dendrogram
Calculating Fowlkes-Mallows index using the profdpm R package
Convert a dendrogram into phylo
Topological Distances Between Two dendrograms
Is the object of class hclust
Raise the height of a dendrogram tree
Creates completely blank theme in ggplot
Tries to run DendSer on a dendrogram
Highlight distint edges in a tree (compared to another one)
Get attributes of dendrogram's nodes
prune_common_subtrees.dendlist
Prune trees to their common subtrees
Global Comparison of two (or more) dendrograms
Remove all nodePar values from a dendrogram's leaves
recursivly apply a function on a list
match_order_dendrogram_by_old_order
Adjust the order of one dendrogram based on another (using order)
Fix rank of leaves order values in a dendrogram
Get the colors of the branches of a dendrogram's leaves