Extending 'dendrogram' Functionality in R
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘dendextend’ version 1.17.1
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
A B C D E F G H I K L M N O P R S T U W
| dendextend-package | Functions for extending dendrogram objects |
-- A --
| all.equal.dendlist | Global Comparison of two (or more) dendrograms |
| 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.ggdend | Creates dendrogram plot using ggplot. |
| as.ggdend.dendrogram | Creates dendrogram plot using ggplot. |
| 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 |
| as_hclust_fixed | Convert dendrogram Objects to Class hclust |
-- B --
| 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 dendrogram |
| Bk_plot | Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's |
| 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 |
| branches_color | Color tree's branches according to sub-clusters |
-- C --
| circlize_dendrogram | Plot a circlized dendrograms |
| click_rotate | Interactively rotate a tree object |
| click_rotate.default | Interactively rotate a tree object |
| click_rotate.dendrogram | 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 |
| colored_bars | Add colored bars to a dendrogram |
| colored_dots | Add colored dots beside a dendrogram |
| 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 |
| colour_branches | Color tree's branches according to sub-clusters |
| colour_labels | Color dend's labels according to sub-clusters |
| common_subtrees_clusters | Find clusters of common subtrees |
| cor.dendlist | Correlation matrix between a list of trees. |
| cor_bakers_gamma | Baker's Gamma correlation coefficient |
| cor_bakers_gamma.default | Baker's Gamma correlation coefficient |
| cor_bakers_gamma.dendlist | Baker's Gamma correlation coefficient |
| cor_bakers_gamma.dendrogram | Baker's Gamma correlation coefficient |
| cor_bakers_gamma.hclust | Baker's Gamma correlation coefficient |
| cor_common_nodes | Proportion of commong nodes between two trees |
| cor_cophenetic | Cophenetic correlation between two trees |
| cor_cophenetic.default | Cophenetic correlation between two trees |
| cor_cophenetic.dendlist | Cophenetic correlation between two trees |
| cor_FM_index | Correlation of FM_index for some k |
| count_terminal_nodes | Counts the number of terminal nodes (merging 0 nodes!) |
| cutree | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.agnes | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.default | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.dendrogram | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.diana | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.hclust | Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data |
| cutree.phylo | 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!) |
| cut_lower_fun | Cut a dendrogram - and run a function on the output |
-- D --
| dendbackback | Tanglegram plot |
| dendextend | Functions for extending dendrogram objects |
| dendextend_cut_lower_fun | Cut a dendrogram - and run a function on the output |
| dendextend_heights_per_k.dendrogram | Which height will result in which k for a dendrogram |
| dendextend_options | Access to dendextend_options |
| dendlist | Creating a dendlist object from several dendrograms |
| DendSer.dendrogram | Tries to run DendSer on a dendrogram |
| dend_diff | Plots two trees side by side, highlighting edges unique to each tree in red. |
| dend_diff.dendlist | Plots two trees side by side, highlighting edges unique to each tree in red. |
| dend_diff.dendrogram | Plots two trees side by side, highlighting edges unique to each tree in red. |
| dend_expend | Finds a "good" dendrogram for a dist |
| 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 |
-- E --
| entanglement | Measures entanglement between two trees |
| entanglement.dendlist | Measures entanglement between two trees |
| entanglement.dendrogram | Measures entanglement between two trees |
| entanglement.hclust | Measures entanglement between two trees |
| entanglement.phylo | Measures entanglement between two trees |
-- F --
| fac2num | Turns a factor into a number |
| find_dend | Finds a "good" dendrogram for a dist |
| 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 |
| FM_index | Calculating Fowlkes-Mallows Index |
| FM_index_permutation | Calculating Fowlkes-Mallows Index under H0 |
| FM_index_R | Calculating Fowlkes-Mallows index in R |
-- G --
| 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. |
| ggplot.dendrogram | Creates dendrogram plot using ggplot. |
| ggplot.ggdend | Creates dendrogram plot using ggplot. |
-- H --
| hang.dendrogram | Hang dendrogram leaves |
| has_component_in_attribute | Does a dendrogram has an edgePar/nodePar component? |
| has_edgePar | Does a dendrogram has an edgePar/nodePar component? |
| has_nodePar | 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 line-width |
| highlight_branches_col | Highlight a dendrogram's branches heights via color and line-width |
| highlight_branches_lwd | Highlight a dendrogram's branches heights via color and line-width |
| highlight_distinct_edges | Highlight distint edges in a tree (compared to another one) |
| highlight_distinct_edges.dendlist | Highlight distint edges in a tree (compared to another one) |
| highlight_distinct_edges.dendrogram | Highlight distint edges in a tree (compared to another one) |
-- I --
| identify.dendrogram | Identify Clusters in a Dendrogram (not hclust) |
| intersect_trees | Intersect trees |
| is.dendlist | Is the object of some class |
| is.dendrogram | Is the object of some class |
| is.dist | Is the object of some class |
| is.hclust | Is the object of some class |
| is.natural.number | Check if numbers are natural |
| is.phylo | Is the object of some class |
| is_null_list | Checks if the value is and empty list() |
| is_some_class | Is the object of some class |
-- K --
| khan | Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes. |
-- L --
| labels.hclust | "label" assignment operator |
| labels.phylo | "label" assignment operator |
| labels<- | "label" assignment operator |
| labels<-.default | "label" assignment operator |
| labels<-.dendrogram | "label" assignment operator |
| labels<-.hclust | "label" assignment operator |
| labels<-.phylo | "label" assignment operator |
| labels_cex | Retrieve/assign cex to the labels of a dendrogram |
| labels_cex<- | Retrieve/assign cex to the labels of a dendrogram |
| labels_col | Retrieve/assign colors to the labels of a dendrogram |
| labels_colors | Retrieve/assign colors to the labels of a dendrogram |
| labels_colors<- | Retrieve/assign colors to the labels of a dendrogram |
| ladderize | Ladderize a Tree |
| ladderize.dendlist | Ladderize a Tree |
| ladderize.dendrogram | Ladderize a Tree |
| ladderize.phylo | Ladderize a Tree |
| leaf_Colors | Return the leaf Colors of a dendrogram |
| leaf_colors | Return the leaf Colors of a dendrogram |
| lowest_common_branch | Find lowest common branch were the two items are shared |
-- M --
| 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) |
| max_depth | Find minimum/maximum depth of a dendrogram |
| min_depth | Find minimum/maximum depth of a dendrogram |
-- N --
| na_locf | Last Observation Carried Forward |
| nleaves | Counts the number of leaves in a tree |
| nleaves.default | Counts the number of leaves in a tree |
| nleaves.dendlist | Counts the number of leaves in a tree |
| nleaves.dendrogram | Counts the number of leaves in a tree |
| nleaves.hclust | Counts the number of leaves in a tree |
| nleaves.phylo | Counts the number of leaves in a tree |
| nnodes | Counts the number of nodes (Vertices) in a tree |
| nnodes.default | Counts the number of nodes (Vertices) in a tree |
| nnodes.dendrogram | Counts the number of nodes (Vertices) in a tree |
| nnodes.hclust | Counts the number of nodes (Vertices) in a tree |
| nnodes.phylo | Counts the number of nodes (Vertices) in a tree |
| noded_with_condition | Find which nodes satisfies a condition |
-- O --
| order.dendrogram<- | order.dendrogram<- assignment operator |
| order.hclust | Ordering of the Leaves in a hclust Dendrogram |
-- P --
| partition_leaves | A list with labels for each subtree (edge) |
| place_labels | Set/place new labels in a dendrogram |
| plot.dendlist | Creating a dendlist object from several dendrograms |
| plot.find_k | Find the (estimated) number of clusters for a dendrogram using average silhouette width |
| plot_horiz.dendrogram | Plotting a left-tip-adjusted horizontal dendrogram |
| prepare.ggdend | Creates dendrogram plot using ggplot. |
| print.ggdend | Creates dendrogram plot using ggplot. |
| prune | Prunes a tree (using leaves' labels) |
| prune.default | Prunes a tree (using leaves' labels) |
| prune.dendrogram | Prunes a tree (using leaves' labels) |
| prune.hclust | Prunes a tree (using leaves' labels) |
| prune.phylo | Prunes a tree (using leaves' labels) |
| prune.rpart | 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 |
-- R --
| 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 |
| rev.hclust | Rotate a tree object |
| rllply | recursivly apply a function on a list |
| rotate | Rotate a tree object |
| rotate.default | Rotate a tree object |
| rotate.dendrogram | Rotate a tree object |
| rotate.hclust | Rotate a tree object |
| rotate.phylo | Rotate a tree object |
| rotate_DendSer | Rotates dend based on DendSer |
-- S --
| 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.data.table | Set (/update) features to a dendrogram |
| set.dendlist | Set (/update) features to a dendrogram |
| set.dendrogram | Set (/update) features to a dendrogram |
| set_labels | Set/place new labels in a dendrogram |
| shuffle | Random rotation of trees |
| shuffle.default | Random rotation of trees |
| shuffle.dendlist | Random rotation of trees |
| shuffle.dendrogram | Random rotation of trees |
| shuffle.hclust | Random rotation of trees |
| shuffle.phylo | Random rotation of trees |
| sort.dendlist | Rotate a tree object |
| sort.dendrogram | Rotate a tree object |
| sort.hclust | Rotate a tree object |
| 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 |
-- T --
| tanglegram | Tanglegram plot |
| tanglegram.default | Tanglegram plot |
| tanglegram.dendlist | Tanglegram plot |
| tanglegram.dendrogram | Tanglegram plot |
| tanglegram.hclust | Tanglegram plot |
| tanglegram.phylo | Tanglegram plot |
| theme_dendro | Creates completely blank theme in ggplot |
-- U --
| unbranch | unbranch trees |
| unbranch.default | unbranch trees |
| unbranch.dendrogram | unbranch trees |
| unbranch.hclust | unbranch trees |
| unbranch.phylo | unbranch trees |
| unclass_dend | unclass an entire dendrogram tree |
| untangle | untangle dendrograms |
| untangle.default | untangle dendrograms |
| untangle.dendlist | untangle dendrograms |
| untangle.dendrogram | untangle dendrograms |
| untangle_DendSer | Tries to run DendSer on a dendrogram |
| untangle_labels | untangle dendrograms |
| 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 |
-- W --
| which_leaf | Which node is a leaf? |
| which_node | Which node id is common to a group of labels |