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