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 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 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.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.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 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 which_leaf Which node is a leaf? which_node Which node id is common to a group of labels