gbs.dendro: Constructs dendrogram.

In trife/gbs: Tools for Genotyping-By-Sequencing Data

Description

Creates a custom dendrogram with the ability to color both terminal leafs and nodes based on a separate data frame.

Usage

gbs.dendro(phylo, df, taxa, tips, leafs, tipColors, leafColors,
  leg.title = NULL, leg.cex = 1, leg.color = tipColors, ...)

Arguments

phylo	An object of class phylo.
df	The data frame containing the items to be plotted.
taxa	A string representing the column name in the df dataframe that contains the same names that exist in the geno object.
tips	A string representing the column in the df dataframe that contains the factors to use to color the tips.
leafs	A string representing the column in the df dataframe that contains the factors to use to color the terminal leafs.
leg.title	A string representing the title for the legend.
leg.cex	A numerical value for the size of the legend.
leg.color	The colors to use for the legend (tipColors or leafColors).
...	Additional graphical arguments to pass to the plot.phylo function.
tipColor	A vector of colors to be used for the tips.
leafColor	A vector of colors to be used for the leafs.

Details

This function allows for the independent coloring of both the terminal leafs of a dendrogram as well as the tips based on an a separate data frame.

Author(s)

Trevor Rife, [e-mail]

Narinder Singh, [e-mail]

Examples

data(wheat)
phylo <- as.phylo(hclust(dist(hap$geno)))
gbs.dendro(phylo,phenotypes,taxa="line",tips="type",leafs="group",type="fan",edge.width=2)

trife/gbs documentation built on May 31, 2019, 7:53 p.m.