plotdistmat: Plot genetic distance matrix
In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description Usage Arguments Details See Also Examples

Provides a graphical representation of the pairwise genetic distance matrix for a collection of genomes.

1 2	plotdistmat(distmat, colvec, coltext, pos = "topleft", labels = NULL, numbers = TRUE, ...)

`distmat`	Symmetrical pairwise distance matrix, the [i,j]th entry corresponding to the genetic distance between genomes i and j.
`colvec`	Vector of colors to represent increasing genetic distance.
`coltext`	Vector of colors for numerals representing geentic distance on plot (if `numbers=TRUE`).
`pos`	Position of the matrix in plot. Allowed values are `"topleft"`, `"topright"`, `"bottomleft"` and `"bottomright"`.
`labels`	Axis labels for genomes (by default, marked 1,...,n).
`numbers`	Should the genetic distance be recorded in each cell?
`...`	Additional arguments to be passed to `plot`.

Plots the upper (or lower) diagonal genetic distance matrix, with each entry colored according to geentic distance.

gd

	
data(withinhost)
Gmat <- gd(withinhost$obs.strain, withinhost$libr, withinhost$nuc, 
           withinhost$librstrains)

colvec <- rainbow(1200)[1:1000] # Color palette
coltext <- rep("black", length(colvec)) # Corresponding text colors
coltext[680:970] <- "white" # White text for darker background colours

plotdistmat(Gmat, colvec, coltext, pos="bottomleft", labels=NULL, numbers=TRUE)