genBaRcode: plotClusterTree – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

plotClusterTree

Plotting a Cluster Tree

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

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

`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).

Analysis and Visualization Tools for Genetic Barcode Data

v1.2.4

LGPL

Authors

Lars Thielecke <lars.thielecke@tu-dresden.de>

Initial release