Extending 'Dendrogram' Functionality in R

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 |

depth | Find minimum/maximum depth of 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_dend | Finds a "good" dendrogram for a dist |

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.natural.number | Check if numbers are natural |

is_null_list | Checks if the value is and empty list() |

is_some_class | Is the object of some class |

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... |

pvrect2 | Draw Rectangles Around a Dendrogram's Clusters with High/Low... |

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 |

reindex_dend | Reindexing a pruned dendrogram |

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 |

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