| Functions for extending dendrogram objects | dendextend-package dendextend |
| Rotate tree branches for k | all_couple_rotations_at_k |
| Check if all the elements in a vector are unique | all_unique |
| Global Comparison of two (or more) dendrograms | all.equal.dendlist all.equal.dendrogram |
| Convert dendrogram Objects to Class hclust | as_hclust_fixed |
| Try to coerce something into a dendlist | as.dendlist |
| Convert a dendrogram into phylo | as.phylo.dendrogram |
| Populates dendextend functions into dendextend_options | assign_dendextend_options |
| Assign values to edgePar of dendrogram's branches | assign_values_to_branches_edgePar |
| Assign values to edgePar of dendrogram's leaves | assign_values_to_leaves_edgePar |
| Assign values to nodePar of dendrogram's leaves | assign_values_to_leaves_nodePar |
| Assign values to nodePar of dendrogram's nodes | assign_values_to_nodes_nodePar |
| Bakers Gamma for two k matrices | bakers_gamma_for_2_k_matrix |
| Bk - Calculating Fowlkes-Mallows Index for two dendrogram | Bk |
| Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram | Bk_permutations |
| Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's | Bk_plot |
| Change col/lwd/lty of branches based on clusters | branches_attr_by_clusters |
| Change col/lwd/lty of branches matching labels condition | branches_attr_by_labels |
| Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members | branches_attr_by_lists |
| Plot a circlized dendrograms | circlize_dendrogram |
| Interactively rotate a tree object | click_rotate click_rotate.default click_rotate.dendrogram |
| Collapse branches under a tolerance level | collapse_branch |
| Collapse a sub dendrogram of adjacent labels within a dend | collapse_labels |
| Color tree's branches according to sub-clusters | branches_color color_branches colour_branches |
| Color dend's labels according to sub-clusters | color_labels colour_labels |
| Color unique labels in a dendrogram | color_unique_labels |
| Add colored bars to a dendrogram | colored_bars |
| Add colored dots beside a dendrogram | colored_dots |
| Find clusters of common subtrees | common_subtrees_clusters |
| Baker's Gamma correlation coefficient | cor_bakers_gamma cor_bakers_gamma.default cor_bakers_gamma.dendlist cor_bakers_gamma.dendrogram cor_bakers_gamma.hclust |
| Proportion of commong nodes between two trees | cor_common_nodes |
| Cophenetic correlation between two trees | cor_cophenetic cor_cophenetic.default cor_cophenetic.dendlist |
| Correlation of FM_index for some k | cor_FM_index |
| Correlation matrix between a list of trees. | cor.dendlist |
| Counts the number of terminal nodes (merging 0 nodes!) | count_terminal_nodes |
| Cut a dendrogram - and run a function on the output | cut_lower_fun dendextend_cut_lower_fun |
| Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data | cutree cutree.agnes cutree.default cutree.dendrogram cutree.diana cutree.hclust cutree.phylo |
| cutree for dendrogram (by 1 height only!) | cutree_1h.dendrogram |
| cutree for dendrogram (by 1 k value only!) | cutree_1k.dendrogram |
| Plots two trees side by side, highlighting edges unique to each tree in red. | dend_diff dend_diff.dendlist dend_diff.dendrogram |
| Finds a "good" dendrogram for a dist | dend_expend find_dend |
| Access to dendextend_options | dendextend_options |
| Creating a dendlist object from several dendrograms | dendlist plot.dendlist |
| Tries to run DendSer on a dendrogram | DendSer.dendrogram |
| Turns a dist object to a "long" table | dist_long |
| Topological Distances Between Two dendrograms | dist.dendlist |
| Finds distinct edges in one tree compared to another | distinct_edges |
| Duplicate a leaf X times | duplicate_leaf |
| Measures entanglement between two trees | entanglement entanglement.dendlist entanglement.dendrogram entanglement.hclust entanglement.phylo |
| Turns a factor into a number | fac2num |
| Search for the sub-dendrogram structure composed of selected labels | find_dendrogram |
| Find the (estimated) number of clusters for a dendrogram using average silhouette width | find_k plot.find_k |
| Fix members attr in a dendrogram | fix_members_attr.dendrogram |
| Flatten the branches of a dendrogram's root | flatten.dendrogram |
| Flip leaves | flip_leaves |
| Calculating Fowlkes-Mallows Index | FM_index |
| Calculating Fowlkes-Mallows Index under H0 | FM_index_permutation |
| Calculating Fowlkes-Mallows index in R | FM_index_R |
| Get height attributes from a dendrogram | get_branches_heights |
| Get height attributes from a dendrogram's children | get_childrens_heights |
| Get/set attributes of dendrogram's leaves | get_leaves_attr |
| Get an attribute of the branches of a dendrogram's leaves | get_leaves_branches_attr |
| Get the colors of the branches of a dendrogram's leaves | get_leaves_branches_col |
| Get edgePar of dendrogram's leaves | get_leaves_edgePar |
| Get nodePar of dendrogram's leaves | get_leaves_nodePar |
| Get attributes of dendrogram's nodes | get_nodes_attr |
| Get the x-y coordinates of a dendrogram's nodes | get_nodes_xy |
| get attributes from the dendrogram's root(!) branches | get_root_branches_attr |
| Extract a list of _k_ subdendrograms from a given dendrogram object | get_subdendrograms |
| Creates dendrogram plot using ggplot. | as.ggdend as.ggdend.dendrogram ggdend ggplot.dendrogram ggplot.ggdend prepare.ggdend print.ggdend |
| Hang dendrogram leaves | hang.dendrogram |
| Does a dendrogram has an edgePar/nodePar component? | has_component_in_attribute has_edgePar has_nodePar |
| Which height will result in which k for a dendrogram | dendextend_heights_per_k.dendrogram heights_per_k.dendrogram |
| Highlight a dendrogram's branches heights via color and line-width | highlight_branches highlight_branches_col highlight_branches_lwd |
| Highlight distint edges in a tree (compared to another one) | highlight_distinct_edges highlight_distinct_edges.dendlist highlight_distinct_edges.dendrogram |
| Identify Clusters in a Dendrogram (not hclust) | identify.dendrogram |
| Intersect trees | intersect_trees |
| Checks if the value is and empty list() | is_null_list |
| Is the object of some class | is.dendlist is.dendrogram is.dist is.hclust is.phylo is_some_class |
| Check if numbers are natural | is.natural.number |
| Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes. | khan |
| Retrieve/assign cex to the labels of a dendrogram | labels_cex labels_cex<- |
| Retrieve/assign colors to the labels of a dendrogram | labels_col labels_colors labels_colors<- |
| "label" assignment operator | labels.hclust labels.phylo labels<- labels<-.default labels<-.dendrogram labels<-.hclust labels<-.phylo |
| Ladderize a Tree | ladderize ladderize.dendlist ladderize.dendrogram ladderize.phylo |
| Return the leaf Colors of a dendrogram | leaf_Colors leaf_colors |
| Find lowest common branch were the two items are shared | lowest_common_branch |
| Adjust the order of one dendrogram based on another (using labels) | match_order_by_labels |
| Adjust the order of one dendrogram based on another (using order) | match_order_dendrogram_by_old_order |
| Find minimum/maximum depth of a dendrogram | max_depth min_depth |
| Last Observation Carried Forward | na_locf |
| Counts the number of leaves in a tree | nleaves nleaves.default nleaves.dendlist nleaves.dendrogram nleaves.hclust nleaves.phylo |
| Counts the number of nodes (Vertices) in a tree | nnodes nnodes.default nnodes.dendrogram nnodes.hclust nnodes.phylo |
| Find which nodes satisfies a condition | noded_with_condition |
| order.dendrogram<- assignment operator | order.dendrogram<- |
| Ordering of the Leaves in a hclust Dendrogram | order.hclust |
| A list with labels for each subtree (edge) | partition_leaves |
| Plotting a left-tip-adjusted horizontal dendrogram | plot_horiz.dendrogram |
| Prunes a tree (using leaves' labels) | prune prune.default prune.dendrogram prune.hclust prune.phylo prune.rpart |
| Prune trees to their common subtrees | prune_common_subtrees.dendlist |
| Trims one leaf from a dendrogram | prune_leaf |
| Get Pvclust Edges Information | pvclust_edges |
| The significant branches in a dendrogram, based on a pvclust object | pvclust_show_signif |
| Significance gradient of branches in a dendrogram (via pvclust) | pvclust_show_signif_gradient |
| Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values | pvrect2 |
| Raise the height of a dendrogram tree | raise.dendrogram |
| Rank branches' heights | rank_branches |
| Fix rank of leaves order values in a dendrogram | rank_order.dendrogram |
| Rank a vector based on clusters | rank_values_with_clusters |
| Draw Rectangles Around a Dendrogram's Clusters | rect.dendrogram |
| Reindexing a pruned dendrogram | reindex_dend |
| Remove all edgePar values from a dendrogram's branches | remove_branches_edgePar |
| Remove all nodePar values from a dendrogram's leaves | remove_leaves_nodePar |
| Remove all nodePar values from a dendrogram's nodes | remove_nodes_nodePar |
| recursivly apply a function on a list | rllply |
| Rotate a tree object | rev.hclust rotate rotate.default rotate.dendrogram rotate.hclust rotate.phylo sort.dendlist sort.dendrogram sort.hclust |
| Rotates dend based on DendSer | rotate_DendSer |
| Sample a tree | sample.dendrogram |
| Rotates a dendrogram based on a seriation of a distance matrix | seriate_dendrogram |
| Set (/update) features to a dendrogram | set set.data.table set.dendlist set.dendrogram |
| Set/place new labels in a dendrogram | place_labels set_labels |
| Random rotation of trees | shuffle shuffle.default shuffle.dendlist shuffle.dendrogram shuffle.hclust shuffle.phylo |
| Sorts two clusters vector by their names | sort_2_clusters_vectors |
| Sorts a distance matrix by rows and columns names | sort_dist_mat |
| Sort the values level in a vector | sort_levels_values |
| Tanglegram plot | dendbackback tanglegram tanglegram.default tanglegram.dendlist tanglegram.dendrogram tanglegram.hclust tanglegram.phylo |
| Creates completely blank theme in ggplot | theme_dendro |
| unbranch trees | unbranch unbranch.default unbranch.dendrogram unbranch.hclust unbranch.phylo |
| unclass an entire dendrogram tree | unclass_dend |
| untangle dendrograms | untangle untangle.default untangle.dendlist untangle.dendrogram untangle_labels |
| Tries to run DendSer on a dendrogram | untangle_DendSer |
| Untangle - random search | untangle_random_search |
| Stepwise untangle one tree compared to another | untangle_step_rotate_1side |
| Stepwise untangle two trees one at a time | untangle_step_rotate_2side |
| Stepwise untangle two trees at the same time | untangle_step_rotate_both_side |
| Which node is a leaf? | which_leaf |
| Which node id is common to a group of labels | which_node |
