plot.lsmodel.tm: Make a bubble plot of a lineage-specific transition matrix of...
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Author(s) Examples

Make a bubble plot of a lineage-specific transition matrix of a tree model.

## S3 method for class 'lsmodel.tm'
plot(x, i = 1, show.eq.freq = TRUE, max.cex = 10,
  eq.freq.max.cex = 5, alphabet = NULL, col = NULL, eq.freq.col = NULL,
  filled = TRUE, add = FALSE, ...)

`x`	An object of type `tm`.
`i`	An integer identifying which element of tm[["ls.model"]] to plot.
`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`.

Melissa J. Hubisz

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
filename <- "rev.mod"
unzip(exampleArchive, filename)
tm <- read.tm(filename)
tm <- add.ls.mod(tm, branch="mm9", subst.mod="HKY85")
plot.lsmodel.tm(tm, 1)
tm$ls.model$backgd <- c(0.9, 0.05, 0.03, 0.02)
plot.lsmodel.tm(tm, 1)
plot.rate.matrix(tm[["rate.matrix"]],
                 eq.freq=tm[["backgd"]],
                 filled=FALSE,
                 alphabet=tm[["alphabet"]])
unlink(filename)