tree_time: Plot Phylogenies and Time

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

Description

These two functions plot a tree built from the sequences availabl in the obkData object together with the time of sampling of each sequence (also taken from the same object).

Usage

tree_time_1(x)
tree_time_2(x)

Arguments

x	an obkData object.

Details

The first function tree_time_1 plots the NJ tree growing upwards, without the branch length information, and the time axis is represented on top with from left to right. The second function tree_time_2 plots the NJ tree in the usual way, from left to right, with the branch length information, and the time axis is represented on bottom also from left to right.

Coloured lines show the link between the tips of the tree (i.e., unique sequences) and the time of sampling of the individuals. The colour scale goes from blue (oldest dates) to red (youngest dates).

The functions scan 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.

Note

The neighbor-joigning (NJ) method reconstructs unrooted trees whereas the present functions represent them as rooted.

Author(s)

Emmanuel Paradis

Examples

## Not run: 
data(ToyOutbreak)
tree_time_1(ToyOutbreak)
tree_time_2(ToyOutbreak)

## End(Not run)

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