Perform Hierarchical Clustering and tree pruning on a phylogenetic tree

The phylogenetic tree is pruned with cutreeDynamic to get clusters.

Usage

tree2clusters(
  treeStr,
  treeDistances = NULL,
  treeLabels = NULL,
  cutHeight = NULL,
  minClusterSize = 1,
  extra = TRUE,
  verbose = FALSE
)

Arguments

treeStr

A character vector of a phylogenetic tree in Newick format

treeDistances

numeric matrix of distances, that were used to generate the tree. If NULL, it will be inferred from tree branch lengths.

treeLabels

A character vector of tree leaf labels.

cutHeight

Define at which height to cut tree. Default automatically defined.

minClusterSize

Minimum size of clusters. Default 1.

extra

Boolean whether to use extra parameters for the cutreeDynamic.

verbose

Logical. If TRUE, enables verbose output from the Java backend.

Value

• character vector of the clusters. Each row contains data for a cluster, separated by space. The id of the cluster, the size of the cluster (number of elements) and the names of its elements, Cluster id 0 contains all the objects not assigned to a cluster (singletons). Example clusters output :

  0	3	Sample1	Sample2	Sample3
  1	3	Sample4	Sample5	Sample6
  2	2	Sample7	Sample8
  3	2	Sample9	Sample0

References

Java implementation: https://github.com/gkanogiannis/BioInfoJava-Utils

Author

Anestis Gkanogiannis, anestis@gkanogiannis.com

Examples

my.clust <- tree2clusters(
    treeStr = dist2tree(
        inputDist = system.file("extdata", "samples.vcf.dist.gz",
            package = "fastreeR"
        )
    ),
    verbose = TRUE
)
#>  ..cutHeight not given, setting it to 0.0793  ===>  99% of the (truncated) height range in dendro.
#>  ..done.