upgma: Draws a hierarchical clustering tree (UPGMA).

In BinMat: Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs)

Draws a hierarchical clustering tree (UPGMA).

Description

Creates a UPGMA hierarchical clustering tree, with a specified number of bootstrap repetitions.

Usage

upgma(
  x,
  bts = 10,
  size = 0.55,
  lab_size = 0.55,
  method = "binary",
  hclust = "average",
  fromFile = FALSE
)

Arguments

x	Consolidated binarx matrix.
bts	Bootstrap replications. Set to 10 by default.
size	Size of plot. Set to 0.55 by default.
lab_size	Size of label text. Set to 0.55 by default.
method	Distance method. Set to 'binary' (=Jaccard distance) by default.
hclust	Clustering method. Set to 'average' (=UPGMA) by default
fromFile	Indicates whether the binary data used by the function has been consolidated by BinMat, or whether it comes from the user's own file. Set to FALSE by default (in the assumption that the data has been consolidated by BinMat, and that that object is being passed to the function).

Value

UPGMA tree

Examples

data(BinMatInput_reps)
mat = BinMatInput_reps
cons = consolidate(mat)
clust = upgma(cons)

BinMat documentation built on March 18, 2022, 7:05 p.m.