- dendextend: Extending R's Dendrogram Functionality
- is.natural.number: Check if numbers are natural
Check if numbers are natural
Vectorized function for checking if numbers are natural or not. Helps in checking if a vector is of type "order".
a vector of numbers
tolerence to floating point issues.
(not currently in use)
logical - is the entered number natural or not.
Marco Gallotta (a.k.a: marcog), Tal Galili
This function was written by marcog, as an answer to my question here: http://stackoverflow.com/questions/4562257/what-is-the-fastest-way-to-check-if-a-number-is-a-positive-natural-number-in-r
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- all_couple_rotations_at_k: Rotate tree branches for k
- all.equal.dendrogram: Global Comparison of two (or more) dendrograms
- all_unique: Check if all the elements in a vector are unique
- as.dendlist: Try to coerce something into a dendlist
- as_hclust_fixed: Convert dendrogram Objects to Class hclust
- 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
- 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...
- Bk_plot: Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram...
- 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
- colored_bars: Add colored bars to a dendrogram
- color_labels: Color dend's labels according to sub-clusters
- color_unique_labels: Color unique labels in a dendrogram
- common_subtrees_clusters: Find clusters of common subtrees
- 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
- cor.dendlist: Correlation matrix between a list of trees.
- cor_FM_index: Correlation of FM_index for some k
- 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_1h.dendrogram: cutree for dendrogram (by 1 height only!)
- cutree_1k.dendrogram: cutree for dendrogram (by 1 k value only!)
- cutree-methods: Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data
- d3dendrogram: Plot dendrogram to webpage and view.
- d3dendro_options: Get or set current defaults for d3dendrogram
- dend_diff: Plots two trees side by side, highlighting edges unique to...
- dendextend_labels.dendrogram: Labels of the Leaves in a Dendrogram
- dendextend_options: Access to dendextend_options
- dendextend-package: Functions for extending dendrogram objects
- dendlist: Creating a dendlist object from several dendrograms
- DendSer.dendrogram: Tries to run DendSer on a dendrogram
- 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
- entanglement: Measures entanglement between two trees
- fac2num: Turns a factor into a number
- find_k: Find the (estimated) number of clusters for a dendrogram...
- 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_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_null_list: Checks if the value is and empty list()
- is.phylo: Is the object of class phylo
- khan: Microarray gene expression dataset from Khan et al., 2001....
- labels-assign: "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...
- match_order_dendrogram_by_old_order: Adjust the order of one dendrogram based on another (using...
- 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-assign: 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...
- pvclust_show_signif_gradient: Significance gradient of branches in a dendrogram (via...
- 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
- reexports: Objects exported from other packages
- 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...
- 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