plot.tm: Make a bubble plot of the transition matrix for a tree model.

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Make a bubble plot of the transition matrix for a tree model.

Usage

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

Arguments

x	An object of type tm.
show.eq.freq	If TRUE, show bubbles representing equilibrium frequencies along the bottom of plot.
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	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.

Author(s)

Melissa J. Hubisz

Examples

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
filename <- "rev.mod"
unzip(exampleArchive, filename)
tm <- read.tm(filename)
plot(tm)
plot(tm, show.eq.freq=FALSE)
plot(tm, max.cex=20, eq.freq.max.cex=1,
     col=matrix(1:16, nrow=4),
     eq.freq.col=c("red", "green"),
     filled=TRUE, add=TRUE)
plot.rate.matrix(tm[["rate.matrix"]],
                 eq.freq=tm[["backgd"]],
                 filled=FALSE)
plot.rate.matrix(tm[["rate.matrix"]],
                 eq.freq=tm[["backgd"]],
                 filled=TRUE, add=TRUE)
unlink(filename)

Example output

rphast documentation built on May 1, 2019, 9:26 p.m.