Man pages for dendextend
Extending 'dendrogram' Functionality in R

all_couple_rotations_at_kRotate tree branches for k
all.equal.dendrogramGlobal Comparison of two (or more) dendrograms
all_uniqueCheck if all the elements in a vector are unique
as.dendlistTry to coerce something into a dendlist
as_hclust_fixedConvert dendrogram Objects to Class hclust
as.phylo.dendrogramConvert a dendrogram into phylo
assign_dendextend_optionsPopulates dendextend functions into dendextend_options
assign_values_to_branches_edgeParAssign values to edgePar of dendrogram's branches
assign_values_to_leaves_edgeParAssign values to edgePar of dendrogram's leaves
assign_values_to_leaves_nodeParAssign values to nodePar of dendrogram's leaves
assign_values_to_nodes_nodeParAssign values to nodePar of dendrogram's nodes
bakers_gamma_for_2_k_matrixBakers Gamma for two k matrices
BkBk - Calculating Fowlkes-Mallows Index for two dendrogram
Bk_permutationsBk permutation - Calculating Fowlkes-Mallows Index for two...
Bk_plotBk plot - ploting the Fowlkes-Mallows Index of two dendrogram...
branches_attr_by_clustersChange col/lwd/lty of branches based on clusters
branches_attr_by_labelsChange col/lwd/lty of branches matching labels condition
branches_attr_by_listsChange col/lwd/lty of branches from the root down to clusters...
circlize_dendrogramPlot a circlized dendrograms
click_rotateInteractively rotate a tree object
collapse_branchCollapse branches under a tolerance level
collapse_labelsCollapse a sub dendrogram of adjacent labels within a dend
color_branchesColor tree's branches according to sub-clusters
colored_barsAdd colored bars to a dendrogram
colored_dotsAdd colored dots beside a dendrogram
color_labelsColor dend's labels according to sub-clusters
color_unique_labelsColor unique labels in a dendrogram
common_subtrees_clustersFind clusters of common subtrees
cor_bakers_gammaBaker's Gamma correlation coefficient
cor_common_nodesProportion of commong nodes between two trees
cor_copheneticCophenetic correlation between two trees
cor.dendlistCorrelation matrix between a list of trees.
cor_FM_indexCorrelation of FM_index for some k
count_terminal_nodesCounts the number of terminal nodes (merging 0 nodes!)
cut_lower_funCut a dendrogram - and run a function on the output
cutree_1h.dendrogramcutree for dendrogram (by 1 height only!)
cutree_1k.dendrogramcutree for dendrogram (by 1 k value only!)
cutree-methodsCut a Tree (Dendrogram/hclust/phylo) into Groups of Data
dend_diffPlots two trees side by side, highlighting edges unique to...
dendextend_optionsAccess to dendextend_options
dendextend-packageFunctions for extending dendrogram objects
dendlistCreating a dendlist object from several dendrograms
DendSer.dendrogramTries to run DendSer on a dendrogram
depthFind minimum/maximum depth of a dendrogram
dist.dendlistTopological Distances Between Two dendrograms
distinct_edgesFinds distinct edges in one tree compared to another
dist_longTurns a dist object to a "long" table
duplicate_leafDuplicate a leaf X times
entanglementMeasures entanglement between two trees
fac2numTurns a factor into a number
find_dendFinds a "good" dendrogram for a dist
find_dendrogramSearch for the sub-dendrogram structure composed of selected...
find_kFind the (estimated) number of clusters for a dendrogram...
fix_members_attr.dendrogramFix members attr in a dendrogram
flatten.dendrogramFlatten the branches of a dendrogram's root
flip_leavesFlip leaves
FM_indexCalculating Fowlkes-Mallows Index
FM_index_permutationCalculating Fowlkes-Mallows Index under H0
FM_index_RCalculating Fowlkes-Mallows index in R
get_branches_heightsGet height attributes from a dendrogram
get_childrens_heightsGet height attributes from a dendrogram's children
get_leaves_attrGet/set attributes of dendrogram's leaves
get_leaves_branches_attrGet an attribute of the branches of a dendrogram's leaves
get_leaves_branches_colGet the colors of the branches of a dendrogram's leaves
get_leaves_edgeParGet edgePar of dendrogram's leaves
get_leaves_nodeParGet nodePar of dendrogram's leaves
get_nodes_attrGet attributes of dendrogram's nodes
get_nodes_xyGet the x-y coordinates of a dendrogram's nodes
get_root_branches_attrget attributes from the dendrogram's root(!) branches
get_subdendrogramsExtract a list of _k_ subdendrograms from a given dendrogram...
ggdendCreates dendrogram plot using ggplot.
hang.dendrogramHang dendrogram leaves
has_component_in_attributeDoes a dendrogram has an edgePar/nodePar component?
heights_per_k.dendrogramWhich height will result in which k for a dendrogram
highlight_branchesHighlight a dendrogram's branches heights via color and...
highlight_distinct_edgesHighlight distint edges in a tree (compared to another one)
identify.dendrogramIdentify Clusters in a Dendrogram (not hclust)
intersect_treesIntersect trees
is.natural.numberCheck if numbers are natural
is_null_listChecks if the value is and empty list()
is_some_classIs the object of some class
khanMicroarray gene expression dataset from Khan et al., 2001....
labels-assign"label" assignment operator
labels_cexRetrieve/assign cex to the labels of a dendrogram
labels_colorsRetrieve/assign colors to the labels of a dendrogram
ladderizeLadderize a Tree
leaf_ColorsReturn the leaf Colors of a dendrogram
lowest_common_branchFind lowest common branch were the two items are shared
match_order_by_labelsAdjust the order of one dendrogram based on another (using...
match_order_dendrogram_by_old_orderAdjust the order of one dendrogram based on another (using...
na_locfLast Observation Carried Forward
nleavesCounts the number of leaves in a tree
nnodesCounts the number of nodes (Vertices) in a tree
noded_with_conditionFind which nodes satisfies a condition
order.dendrogram-assignorder.dendrogram<- assignment operator
order.hclustOrdering of the Leaves in a hclust Dendrogram
partition_leavesA list with labels for each subtree (edge)
plot_horiz.dendrogramPlotting a left-tip-adjusted horizontal dendrogram
prunePrunes a tree (using leaves' labels)
prune_common_subtrees.dendlistPrune trees to their common subtrees
prune_leafTrims one leaf from a dendrogram
pvclust_edgesGet Pvclust Edges Information
pvclust_show_signifThe significant branches in a dendrogram, based on a pvclust...
pvclust_show_signif_gradientSignificance gradient of branches in a dendrogram (via...
pvrect2Draw Rectangles Around a Dendrogram's Clusters with High/Low...
raise.dendrogramRaise the height of a dendrogram tree
rank_branchesRank branches' heights
rank_order.dendrogramFix rank of leaves order values in a dendrogram
rank_values_with_clustersRank a vector based on clusters
rect.dendrogramDraw Rectangles Around a Dendrogram's Clusters
reexportsObjects exported from other packages
reindex_dendReindexing a pruned dendrogram
remove_branches_edgeParRemove all edgePar values from a dendrogram's branches
remove_leaves_nodeParRemove all nodePar values from a dendrogram's leaves
remove_nodes_nodeParRemove all nodePar values from a dendrogram's nodes
rllplyrecursivly apply a function on a list
rotateRotate a tree object
rotate_DendSerRotates dend based on DendSer
sample.dendrogramSample a tree
seriate_dendrogramRotates a dendrogram based on a seriation of a distance...
setSet (/update) features to a dendrogram
set_labelsSet/place new labels in a dendrogram
shuffleRandom rotation of trees
sort_2_clusters_vectorsSorts two clusters vector by their names
sort_dist_matSorts a distance matrix by rows and columns names
sort_levels_valuesSort the values level in a vector
tanglegramTanglegram plot
theme_dendroCreates completely blank theme in ggplot
unbranchunbranch trees
unclass_dendunclass an entire dendrogram tree
untangleuntangle dendrograms
untangle_DendSerTries to run DendSer on a dendrogram
untangle_random_searchUntangle - random search
untangle_step_rotate_1sideStepwise untangle one tree compared to another
untangle_step_rotate_2sideStepwise untangle two trees one at a time
which_leafWhich node is a leaf?
which_nodeWhich node id is common to a group of labels
dendextend documentation built on March 31, 2023, 10:17 p.m.