genBaRcode (version 1.2.8)

plotClusterGgTree: 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")

Value

a ggtree object.

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).

Examples

if (FALSE) {
data(BC_dat)
plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
}