plot.HMM {aphid} | R Documentation |
Plot standard hidden Markov models.
Description
plot.HMM
provides a visual representation of a standard hidden Markov
model.
Usage
## S3 method for class 'HMM'
plot(x, just = "center", arrexp = 1, textexp = 1, begin = FALSE, ...)
Arguments
x |
an object of class |
just |
a character string giving the justfication of the plot relative to the device. Accepted values are "left", "center" and "right". |
arrexp |
the expansion factor to be applied to the arrows in the plot. |
textexp |
the expansion factor to be applied to the text in the plot. |
begin |
logical indicating whether the begin/end state should be plotted. Defaults to FALSE. |
... |
additional arguments to be passed to |
Details
"plot.HMM"
Plots a "HMM"
object as a directed graph.
States (rectangles) are interconnected by directed
lines with line-weights proportional to the transition probabilities between
the states.
Value
NULL (invisibly).
Author(s)
Shaun Wilkinson
References
Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, United Kingdom.
Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, United Kingdom.
See Also
Examples
## the dishonest casino example from Durbin et al (1998)
states <- c("Begin", "Fair", "Loaded")
residues = paste(1:6)
A <- matrix(c(0, 0, 0, 0.99, 0.95, 0.1, 0.01, 0.05, 0.9), nrow = 3)
dimnames(A) <- list(from = states, to = states)
E <- matrix(c(rep(1/6, 6), rep(1/10, 5), 1/2), nrow = 2, byrow = TRUE)
dimnames(E) <- list(states = states[-1], residues = residues)
x <- structure(list(A = A, E = E), class = "HMM")
plot(x, main = "Dishonest casino hidden Markov model")