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 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 branches_attr_by_lists Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members circlize_dendrogram Plot a circlized dendrograms click_rotate Interactively rotate a tree object collapse_branch Collapse branches under a tolerance level collapse_labels Collapse a sub dendrogram of adjacent labels within a dend 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 colored_dots Add colored dots beside 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!) dend_diff Plots two trees side by side, highlighting edges unique to each tree in red. dend_expend Finds a "good" dendrogram for a dist dendextend-package Functions for extending dendrogram objects 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 find_dendrogram Search for the sub-dendrogram structure composed of selected labels find_k Find the (estimated) number of clusters for a dendrogram using average silhouette width 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 get_subdendrograms Extract a list of _k_ subdendrograms from a given dendrogram object 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_col Highlight a dendrogram's branches heights via color and line-width 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. 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) min_depth Find minimum/maximum depth of a dendrogram 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_edges Get Pvclust Edges Information 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) pvrect2 Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values 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 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 matrix 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 untangle_step_rotate_both_side Stepwise untangle two trees at the same time which_leaf Which node is a leaf? which_node Which node id is common to a group of labels