plotClusterTree: Plotting a Cluster Tree

In genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

Plotting a Cluster Tree

Description

Generates a tree plot based on a herachical clustering of the complete distance matrix.

Usage

plotClusterTree(
  BC_dat,
  tree_est = "NJ",
  type = "unrooted",
  tipLabel = FALSE,
  m = "hamming"
)

Arguments

BC_dat	a BCdat object.
tree_est	a character string, indicating the particular cluster algorithm, possible algorithms are "Neighbor-Joining" ("NJ") and "Unweighted Pair Group Method" ("UPGMA").
type	a character string, the graph layout style ("unrooted", "phylogram", "cladogram", "fan", "radial").
tipLabel	a logical value, indicating the use of labeled tree leaves.
m	a character string, Method for distance calculation, default value is Hamming distance. Possible values are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function of the stringdist-package for more information).

genBaRcode documentation built on June 24, 2024, 5:15 p.m.