upgma: Draws a hierarchical clustering tree (UPGMA).

Description Usage Arguments Value Examples

View source: R/upgma.R

Description

Creates an unweighted pair group method with arithmetic mean (UPGMA) hierarchical clustering tree, with a specified number of bootstrap repetitions.

Usage

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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

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

BinMat documentation built on March 13, 2020, 3:11 a.m.