# plot: Plotting of "contDist" Objects In 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

 ```1 2 3 4 5 6``` ```## 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17``` ```## 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) ```