#' Plot a transmission tree
#' @param ttree Transmission tree
#' @param w.shape Shape parameter of the Gamma probability density function representing the generation time
#' @param w.scale Scale parameter of the Gamma probability density function representing the generation time
#' @param showLabels Whether or not to show the labels
#' @param maxTime Maximum value of time to show on x axis
#' @export
plotTTree = function(ttree,w.shape,w.scale,showLabels=TRUE,maxTime=NA) {
nam=ttree$nam
ttree=ttree$ttree
n=nrow(ttree)
#Determine ys
ys <- rep(0, n)
scale <- rep(1,n)
todo=c(which(ttree[,3]==0))
while (length(todo)>0) {
f=which(ttree[,3]==todo[1])
o=rank(-ttree[f,1])
f[o]=f
for (i in f) {ys[i]=ys[todo[1]]+scale[todo[1]]*which(f==i)/(length(f)+1);scale[i]=scale[todo[1]]/(length(f)+1);todo=c(todo,i)}
todo=todo[-1]
}
ys=rank(ys)
par(yaxt='n',bty='n')
mi=min(ttree[,1])
if (is.na(maxTime)) ma=max(ttree[which(!is.na(ttree[,2])),2]) else ma=maxTime
xstep=(ma-mi)/2000
plot(c(),c(),xlim=c(mi-(ma-mi)*0.05,ma+(ma-mi)*0.05),ylim=c(0,n+1),xlab='',ylab='')
maxcol=max(dgamma(seq(0,ma-mi,xstep),shape=w.shape,scale=w.scale))
for (i in 1:n) {
as=seq(ttree[i,1],ma,xstep)
bs=rep(ys[i],length(as))
cs=abs((maxcol-dgamma(as-ttree[i,1],shape=w.shape,scale=w.scale))/maxcol)
cs=gray(cs)
segments(as,bs,x1=as+xstep,col=cs)
points(ttree[i,2],ys[i],col = 'red')
if (showLabels) text(ma+(ma-mi)*0.05,ys[i],nam[i])
if (ttree[i,3]==0) {next}
arrows(ttree[i,1],ys[ttree[i,3]],ttree[i,1],ys[i],length=0.1)
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.