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**dendextend**: Extending R's Dendrogram Functionality**d3dendrogram**: Plot dendrogram to webpage and view.

# Plot dendrogram to webpage and view.

### Description

Plot dendrogram to webpage and view.

### Usage

1 2 |

### Arguments

`d` |
a dendrogram object |

`height` |
pixels, height of the plot. |

`width` |
pixels, width of the plot |

`rightmargin` |
pixels to reserve on the right side for leaf labels. |

`open` |
open the graphic in a browser? (see details). |

`...` |
Graphical options, see |

### Details

If `open=TRUE`

, the graphic is opened using the function defined by `getOption("viewer")`

.
If no `viewer`

option is specified, `utils::browseURL`

is opened. Specifically, in RStudio
this means that the viewer is used.

### Value

If `open=TRUE`

, a character string containing the html is invisibly retured.
If `open=TRUE`

, a character string containing the html is returned.

### Tips

Dendrogram plots with many end-nodes tend to get overlapping labels or (end)nodes. If the number of endnodes is not too large, there are several ways to overcome this.

Decrease font size of the nodes (

`node_font`

, see`d3dendro_options`

on how to specify)Decrease size of node radius (

`node_radius`

,*idem*)Increase the height of the plot. Use about (2 times font height) times count_terminal_nodes(d).

Plot sub-dendrograms in stead of the whole dendrogram. There's only so much detail a screen can display and your eye can observe. Consider plotting subdendrograms or other summaries when dendrograms have many, many nodes.

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.

- 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