A B C D E F G H I L M N O P R S T U
dendextend-package | Functions for extending dendrogram objsects |
all_couple_rotations_at_k | Rotate tree branches for k |
assign_values_to_branches_edgePar | Assign values to edgePar of dendrogram's branches |
assign_values_to_leaves_nodePar | Assign values to nodePar of dendrogram's leaves |
as_hclust_fixed | Convert dendrogram Objects to Class hclust |
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 |
color_branches | Color tree's branches according to sub-clusters |
color_labels | Color tree's labels according to sub-clusters |
colour_branches | Color tree's branches according to sub-clusters |
colour_labels | Color tree's labels according to sub-clusters |
cor_bakers_gamma | Baker's Gamma correlation coefficient |
cor_cophenetic | Cophenetic correlation between two trees |
count_terminal_nodes | Counts the number of terminal nodes (merging 0 nodes!) |
cutree | 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.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 |
dendbackback | Tanglegram plot |
dendextend | Functions for extending dendrogram objsects |
duplicate_leaf | Duplicate a leaf X times |
entanglement | Measures entanglement between two trees |
entanglement.default | 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 |
fac2num | Turns a factor into a number |
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_attr | get attributes from the dendrogram's root branches |
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_nodes_attr | Get attributes of dendrogram's nodes |
hang.dendrogram | Hang dendrogram leaves |
heights_per_k.dendrogram | Which height will result in which k for a dendrogram |
intersect_trees | Intersect trees |
is.dendrogram | Is the object of class dendrogram |
is.hclust | Is the object of class hclust |
is.natural.number | Check if numbers are natural |
is.phylo | Is the object of class phylo |
labels.hclust | "label" assignment operator |
labels.matrix | "label" assignment operator |
labels<- | "label" assignment operator |
labels<-.default | "label" assignment operator |
labels<-.dendrogram | "label" assignment operator |
labels<-.hclust | "label" assignment operator |
labels<-.matrix | "label" assignment operator |
labels_colors | Retrieve/assign colors to the labels of a dendrogram |
labels_colors<- | Retrieve/assign colors to the labels of a dendrogram |
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 |
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) |
nleaves | Counts the number of leaves in a tree |
nleaves.default | 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 |
order.dendrogram<- | order.dendrogram<- assignment operator |
plot_horiz.dendrogram | Plotting a left-tip-adjusted horizontal dendrogram |
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_leaf | Trimms one leaf from a dendrogram |
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 |
remove_branches_edgePar | Remove all edgePar values from a dendrogram's branches |
remove_leaves_nodePar | Remove all nodePar values from a dendrogram's leaves |
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 |
sample.dendrogram | Sample a tree |
shuffle | Random rotation of trees |
shuffle.default | Random rotation of trees |
shuffle.dendrogram | Random rotation of trees |
shuffle.hclust | Random rotation of trees |
shuffle.phylo | Random rotation of trees |
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 |
sort_levels_values | Sort the values level in a vector |
tanglegram | Tanglegram plot |
tanglegram.default | Tanglegram plot |
tanglegram.dendrogram | Tanglegram plot |
tanglegram.hclust | Tanglegram plot |
tanglegram.phylo | Tanglegram plot |
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_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 |