tree_obkData: Plot phylogenies with frequencies of unique sequences

In Hackout2/epiphylo: Epidemics and outbreak dynamics with phylogenetic trees

Description

This function plots a phylogeny built from the unique sequences together with a representation of the abundance (frequencies) of these in the data.

Usage

tree_obkData(x, ncatmax = 10, colfun = topo.colors)

Arguments

x	an obkData object.
ncatmax	an integer giving the number of categories of haplotype frequency.
colfun	a function to define the colours.

Details

First, the unique sequences are extracted using the function haplotype (in pegas). Then, a neighbor-joigning (NJ) tree is built. The tree is plotted on the left-hand side of the graph, and the frequencies of each unique sequence is represented in two ways: coloured labels at the tips of the tree (with the colour scale drawn at the top), and a horizontal barplot on the right-hand side of the graph.

The function scans the data for the different genes and plots the output successively (the user is asked to type enter)

Value

nothing the results are printed on the current graphical device.

Author(s)

Emmanuel Paradis

Examples

## Not run: 
data(ToyOutbreak)
tree_obkData(ToyOutbreak)

## End(Not run)

Hackout2/epiphylo documentation built on May 6, 2019, 9:47 p.m.