plotClusterGgTree: Plotting a Cluster ggTree

In genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

Plotting a Cluster ggTree

Description

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

Usage

plotClusterGgTree(BC_dat, tree_est = "NJ", type = "rectangular", 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 ('rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight').
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).

Value

a ggtree object.

Examples

## Not run: 
data(BC_dat)
plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")

## End(Not run)

genBaRcode documentation built on April 4, 2025, 2:07 a.m.