JSDtree_cluster: Clustering of phylogenies

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Clustering of phylogenies

Description

Clusters phylogenies using hierarchical and k-medoids clustering

Usage

JSDtree_cluster(JSDtree,alpha=0.9,draw=TRUE)

Arguments

JSDtree	a matrix of distances between phylogenie pairs, typically the output of the JSDtree function when the distance is measured as the Jensen-Shannon distance
alpha	the confidence value for demarcating clusters in the hierarchical clustering plot; the default is 0.9
draw	plot heatmap and hierarchical cluster in new windows

Value

plots a heatmap and a hierarchical cluster with bootstrap support, and outputs results of the k-medoids clustering in the form of a list with the following components

clusters	the optimal number of clusters around medoids (see pamk documentation)
cluster_assignments	assignments of trees to clusters
cluster_support	a list with the following components: widths: a table specifying the cluster to which each tree belongs, the neighbor (i.e. most similar) cluster, and the silhouette width of the observation (see silhouette documentation); clus.avg.widths: average silhouette width for each cluster; vg.width: average silhouette width across all clusters

Note

The k-medoids clustering may not work with fewer than 10 trees

Author(s)

E Lewitus

References

Lewitus, E., Morlon, H., Characterizing and comparing phylogenies from their Laplacian spectrum, bioRxiv doi: http://dx.doi.org/10.1101/026476

See Also

JSDtree

Examples

trees<-TESS::tess.sim.age(n=20,age=10,0.15,0.05,MRCA=TRUE)
res<-JSDtree(trees)
JSDtree_cluster(res,alpha=0.9,draw=TRUE)

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.