plot: Plotting of "contDist" Objects

In humburg/tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

Description

Functions for plotting of contDist objects, either directly or as part of contHMM objects.

Usage

## S3 method for class 'contDist'
plot(x, step.size = 0.01, new.plot = TRUE, weight = 1, ...)
## S3 method for class 'tDist'
plot(x, step.size = 0.01, new.plot = TRUE, weight = 1, ...)
## S3 method for class 'contHMM'
plot(x, ...)

Arguments

x	Object of class contDist or contHMM.
step.size	Numeric value indicating the distance between points at which the density function is evaluated.
new.plot	If this is TRUE (the default) a new plot is created, otherwise graph of the density function is added to the current plot.
weight	Weighting factor. The density function will be scaled by this factor. This is useful when plotting mixture components.
...	Additional arguments to be passed to plot

Value

These functions are called for their side effect.

Author(s)

Peter Humburg

See Also

contDist, contHMM

Examples

## create two state HMM with t distributions
state.names <- c("one","two")
transition <- c(0.1, 0.02)
location <- c(1, 2)
scale <- c(1, 1)
df <- c(4, 6)
model <- getHMM(list(a=transition, mu=location, sigma=scale, nu=df),
    state.names)
    
## plot emission distributions of HMM
plot(model)

## now plot density functions separately
par(mfrow=c(1,1))
plot(model@emission$one)
plot(model@emission$two, new.plot=FALSE, lty=2)
legend("topleft", legend=states(model), lty=1:2)

humburg/tileHMM documentation built on May 17, 2019, 9:13 p.m.