transmissionTimeline: plots network diffusion/transmission tree with generation time vs. clock/model time

Description

Plots view of a network with positions determined by the timing and generation depth (previously calculated) in a transmission tree. The horizontal axis is model time, and the vertical axis is the number of steps from the root of the tree.

Usage

transmissionTimeline(x, time.attr, 
                     label, 
                     displaylabels = !missing(label), 
                     label.cex = 0.7, 
                     label.col = 1, 
                     vertex.col = 2, 
                     vertex.border = 1, 
                     vertex.lwd = 1, 
                     vertex.sides = 50, 
                     vertex.cex = 1,
                     jitter=FALSE,
                     edge.col = "gray", 
                     edge.lty = 1, 
                     edge.lwd = 1, 
                     xlab = "time", 
                     ylab = "generation", 
                     ...)

Value

produces a plot, invisibly returns the coordinates of the plot.

Arguments

x: an object than can be coerced into a network. The network must be a tree
time.attr: name of a vertex attribute containing the transmission/infection/diffusion time for each vertex
label: a vector of vertex labels, if desired; defaults to the vertex labels returned by network.vertex.names. If label has one element and it matches with a vertex attribute name, the value of the attribute will be used. Note that labels may be set but hidden by the displaylabels argument.
displaylabels: boolean; should vertex labels be displayed?
label.cex: character expansion factor for label text.
label.col: color for vertex labels; may be given as a vector or a vertex attribute name, if labels are to be of different colors.
vertex.col: color for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different colors.
vertex.border: border color for vertices; may be given as a vector or a vertex attribute name, if vertex borders are to be of different colors.
vertex.lwd: line width of vertex borders; may be given as a vector or a vertex attribute name, if vertex borders are to have different line widths.
vertex.sides: number of polygon sides for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different types. NOTE: only values of 3,4,and 50 (circle) are used as they are translated to pch plot symbols.
vertex.cex: expansion factor for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different sizes.
jitter: if TRUE, noise will be added to the coordinates with jitter to make overlapping vertex positions more noticeable
edge.col: color for edges; may be given as a vector, adjacency matrix, or edge attribute name, if edges are to be of different colors.
edge.lty: line type for edge borders; may be given as a vector, adjacency matrix, or edge attribute name, if edge borders are to have different line types.
edge.lwd: line width scale for edges; May be given as a vector or edge attribute name, if edges are to have different line widths.
xlab: y-axis plot label
ylab: x-axis plot label
...: additional arguments to plot (and par)

Author

skyebend@uw.edu

Details

Many (but not all) of the graphical arguments to plot.network can be used and are expanded in the same way. This does not currently use the plot.network code to draw the network as non-square plot aspect ratios would cause distortion of the vertices when drawn.

Examples

Run this code

# an edgelist describing an infection tree
el <-cbind(c(16, 13, 13,  10, 13, 16, 10, 13, 1, 10, 8, 1, 4, 4, 2, 2),
            1:16)
# a vector of infection times
infectionTimes <- c(583, 494, 634, 40, 712, 701, 224, 719,  
                   674, 0, 749, 621, 453, 665, 709, 575)
# make a network object, include the infection time                   
infTree<-network(el,vertex.attr = list(infectionTimes),
            vertex.attrnames = list('infectionTimes'))

transmissionTimeline(infTree,time.attr='infectionTimes')

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