plot.rate.matrix: Make a bubble plot of a transition matrix
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Make a bubble plot of a transition matrix

## S3 method for class 'rate.matrix'
plot(x, eq.freq = NULL, max.cex = 10,
  eq.freq.max.cex = 5, alphabet = NULL, col = NULL, eq.freq.col = NULL,
  filled = TRUE, add = FALSE, ...)

`x`	A square matrix representing a continuous-time markov model; rows should sum to zero, with negative values cross the diagonal
`eq.freq`	A numeric vector giving the equilibrium frequencies of each state. If provided, the equilibrium frequencies will be plotted along the bottom.
`max.cex`	A scaling factor which determines the size of the largest circle
`eq.freq.max.cex`	A scaling factor which determines the size of the largest circle in the equilibrium frequencies.
`alphabet`	A character vector representing the state names for each row/column of the matrix. Can either be a vector of size `nrow(m)` or a single character string with `nrow(m)` characters. Can also be `NULL` for no row/column labels.
`col`	If `NULL`, all circles will be drawn in black. Otherwise, col can be a matrix of the same dimension of `m`, each entry should indicate the color used for the corresponding cell in the transition matrix.
`eq.freq.col`	(Only applicable when eq.freq provided). Should be vector of same length as eq.freq, though values will be recycled. Values in the vector indicate colors to draw the equilibrium frequency bubbles.
`filled`	If `TRUE`, plot filled circles.
`add`	If `TRUE`, add to the existing plot. Otherwise create a new plot.
`...`	Further arguments to be passed to `plot`.