plotoutbreak: Plot outbreak
In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description Usage Arguments Details Examples

Provides a graphical representation of simulated outbreak and sampled genomes.

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plotoutbreak(epidata, sampledata, col = "red", stack = TRUE, arr.len = 0.1, 
blockheight = 0.5, hspace = max(epidata[,3])/20, labels = NULL, label.pos = "left", 
	block.col = "grey", jitter = 0, pch = 1, ...)

`epidata`	Simulated epidemiological data - matrix consisting of person IDs, infection and recovery times, and infection source.
`sampledata`	Simulated genomic sample data - matrix of person IDs, sample times and genome ID. Genomic sample data simulated with `full=TRUE` cannot be used.
`col`	A vector of colors to represent increasing genetic distance.
`stack`	Should infectious periods be organized to minimize plot height? Alternatively, each period occupies one row.
`arr.len`	Arrow length. See `arrows`.
`blockheight`	The height of each bar representing infectious periods. Takes a value between 0 and 1.
`hspace`	Minimum horizontal space between two infectious period bars (in units of time).
`labels`	Labels for each infectious episode. First columns of `epidata` by default.
`label.pos`	Position of labels. Accepted values are "centre", "left" and "right".
`block.col`	Background color for each infectious period bar.
`jitter`	Amount of jitter to be applied to genome sample points (as a proportion of plot dimensions).
`pch`	Point type for genome samples (see `par`).
`...`	Additional arguments to be passed to `plot`.

Graphical representation of transmission dynamics and sampled genomes. For multiple genome samples per time point, set jitter>0.

data(outbreak)
sampledata <- outbreak$sampledata
epidata <- outbreak$epidata

distmat <- gd(sampledata[,3], outbreak$libr, outbreak$nuc, outbreak$librstrains)

# Now pick colors for sampled isolates
colvec <- rainbow(1200)[1:1000] # Color palette
refnode <- 1 # Compare distance to which isolate?
colv <- NULL # Vector of colors for samples
maxD <- max(distmat[,refnode])

for (i in 1:nrow(sampledata)) {
  	colv <- c(colv, 
              colvec[floor((length(colvec)-1)*(distmat[refnode,i])/maxD)+1])
}

plotoutbreak(epidata, sampledata, col=colv, stack=TRUE, arr.len=0.1, 
             blockheight=0.5, hspace=500, label.pos="left", block.col="grey",
             jitter=0.004, xlab="Time", pch=1)