plotTrans: Plotting a phybreak object transmission tree.

In phybreak: Analysis of Outbreaks with Sequence Data

Description

Plots a phybreak-object as transmission tree. The default is to plot the current state, but any posterior sample can be chosen, as well as various consensus trees; in that case, coloured arrows indicate posterior support.

Usage

plotTrans(x, plot.which = c("sample", "edmonds", "mpc", "mtcc"),
  samplenr = 0, mar = 0.1 + c(4, 0, 0, 0), label.cex = NULL,
  label.space = 0.15, label.adj = 0, arrow.lwd = 1, arrow.length = NULL,
  arrow.col = NULL, sample.pch = 4, sample.lwd = NULL,
  sample.cex = label.cex, polygon.col = "gray", polygon.border = NA,
  line.lty = 3, xlab = "Time", axis.cex = 1, title.cex = 1, ...)

Arguments

x	An object of class phybreak.
plot.which	Either "sample" to plot the current state or a selected posterior sample, "mpc" or "mtcc" to plot a consensus transmission tree (see transtree) or "mcc" to plot the maximum clade credibility tree (see phylotree).
samplenr	If plot.which = "sample", this indicates which posterior tree should be plotted: samplenr = 0 to plot the current state.
mar	Plot margins.
label.cex	Size of host names, as in par("cex"). Defaults to a value between 0.5 and 1 depending on outbreak size.
label.space	Scales the space at the right-hand side to place the host names.
label.adj	Left-right adjustment of host names.
arrow.lwd	Arrow width.
arrow.length	Arrow point length, as default automatically scaled with outbreak size.
arrow.col	Arrow colour. Defaults to "black" if plot.which = sample, and otherwise to five colours c("blue", "green", "orange", "red", "purple") indicating posterior support of infectors in bins of 0.2 width, from low to high support. Any vector of colours will be divided into equal-sized bins.
sample.pch	Character par("pch") used for sampling events.
sample.lwd	Line width of sampling event character.
sample.cex	Size of sampling event character.
polygon.col	Color of polygons indicating generation interval distributions.
polygon.border	Border of polygon.
line.lty	Line type of horizontal host lines.
xlab	X-axis title.
axis.cex	Size of tick labels.
title.cex	Size of X-axis title.
...	Further graphical parameters (see details).

Details

Graphical parameters can be added by using names in the format prefix.parameter for the different parts of the plot. The parameter will then be passed on to the appropriate graphics function, e.g. arrow.lty to change the line type of the arrows. The following prefixes can be used: label for the host labels, arrow for the arrows, sample for the sampling time indicators, polygon for the generation interval distributions, line for the horizontal host lines, axis for the X-axis, and title for the X-axis title.

Author(s)

Don Klinkenberg [e-mail]

References

Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.

Examples

#First build a phybreak-object containing samples.
simulation <- sim.phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation$sequences, times = simulation$sample.times)
MCMCstate <- burnin.phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample.phybreak(MCMCstate, nsample = 50, thin = 2)

plot(MCMCstate, plot.which = "mpc")

phybreak documentation built on May 2, 2019, 3:36 p.m.