Cut a hierarchical tree

This function is designed to work on a hierarchical tree and cut it at user-selected heights. It works with outputs from either hclu_hierarclust or hclust objects. The function allows for cutting the tree based on the chosen number(s) of clusters or specified height(s). Additionally, it includes a procedure to automatically determine the cutting height for the requested number(s) of clusters.

Usage

cut_tree(
  tree,
  n_clust = NULL,
  cut_height = NULL,
  find_h = TRUE,
  h_max = 1,
  h_min = 0,
  dynamic_tree_cut = FALSE,
  dynamic_method = "tree",
  dynamic_minClusterSize = 5,
  dissimilarity = NULL,
  show_hierarchy = FALSE,
  ...
)

Arguments

tree: A bioregion.hierar.tree or an hclust object.
n_clust: An integer vector or a single integer indicating the number of clusters to be obtained from the hierarchical tree, or the output from bioregionalization_metrics(). This should not be used concurrently with cut_height.
cut_height: A numeric vector specifying the height(s) at which the tree should be cut. This should not be used concurrently with n_clust or optim_method.
find_h: A boolean indicating whether the cutting height should be determined for the requested n_clust.
h_max: A numeric value indicating the maximum possible tree height for determining the cutting height when find_h = TRUE.
h_min: A numeric value specifying the minimum possible height in the tree for determining the cutting height when find_h = TRUE.
dynamic_tree_cut: A boolean indicating whether the dynamic tree cut method should be used. If TRUE, n_clust and cut_height are ignored.
dynamic_method: A character string specifying the method to be used for dynamically cutting the tree: either "tree" (clusters searched only within the tree) or "hybrid" (clusters searched in both the tree and the dissimilarity matrix).
dynamic_minClusterSize: An integer indicating the minimum cluster size for the dynamic tree cut method (see dynamicTreeCut::cutreeDynamic()).
dissimilarity: Relevant only if dynamic_method = "hybrid". Provide the dissimilarity data.frame used to build the tree.
show_hierarchy: A boolean specifying if the hierarchy of clusters should be identifiable in the outputs (FALSE by default).
...: Additional arguments passed to dynamicTreeCut::cutreeDynamic() to customize the dynamic tree cut method.

Value

If tree is an output from hclu_hierarclust(), the same object is returned with updated content (i.e., args and clusters). If tree is an hclust object, a data.frame containing the clusters is returned.

Details

The function supports two main methods for cutting the tree. First, the tree can be cut at a uniform height (specified by cut_height or determined automatically for the requested n_clust). Second, the dynamic tree cut method (Langfelder et al., 2008) can be applied, which adapts to the shape of branches in the tree, cutting at varying heights based on cluster positions.

The dynamic tree cut method has two variants:

The tree-based variant (dynamic_method = "tree") uses a top-down approach, relying solely on the tree and the order of clustered objects.
The hybrid variant (dynamic_method = "hybrid") employs a bottom-up approach, leveraging both the tree and the dissimilarity matrix to identify clusters based on dissimilarity among sites. This approach is useful for detecting outliers within clusters.

Note

The find_h argument is ignored if dynamic_tree_cut = TRUE, as cutting heights cannot be determined in this case.

References

Langfelder P, Zhang B & Horvath S (2008) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. BIOINFORMATICS 24, 719-720.

Author

Pierre Denelle (pierre.denelle@gmail.com)
Maxime Lenormand (maxime.lenormand@inrae.fr)
Boris Leroy (leroy.boris@gmail.com)

Examples

comat <- matrix(sample(0:1000, size = 500, replace = TRUE, prob = 1/1:1001),
20, 25)
rownames(comat) <- paste0("Site", 1:20)
colnames(comat) <- paste0("Species", 1:25)

simil <- similarity(comat, metric = "all")
dissimilarity <- similarity_to_dissimilarity(simil)

# User-defined number of clusters
tree1 <- hclu_hierarclust(dissimilarity,
                          n_clust = 5)
#> Building the iterative hierarchical consensus tree... Note that this process can take time especially if you have a lot of sites.
#> Error in if (nrow(dist_matrix) > 2) {    subclusters <- stable_binary_split(dist_matrix, method = method,         n_runs = n_runs, binsplit = "tree")} else {    subclusters <- list(attr(dist_matrix, "Labels")[1], attr(dist_matrix,         "Labels")[2])}: argument is of length zero
tree2 <- cut_tree(tree1, cut_height = .05)
#> Error: object 'tree1' not found
tree3 <- cut_tree(tree1, n_clust = c(3, 5, 10))
#> Error: object 'tree1' not found
tree4 <- cut_tree(tree1, cut_height = c(.05, .1, .15, .2, .25))
#> Error: object 'tree1' not found
tree5 <- cut_tree(tree1, n_clust = c(3, 5, 10), find_h = FALSE)
#> Error: object 'tree1' not found

hclust_tree <- tree2$algorithm$final.tree
#> Error: object 'tree2' not found
clusters_2 <- cut_tree(hclust_tree, n_clust = 10)
#> Error: object 'hclust_tree' not found

cluster_dynamic <- cut_tree(tree1, dynamic_tree_cut = TRUE,
                            dissimilarity = dissimilarity)
#> Error: object 'tree1' not found