plot.DNAcopy {cghMCR} | R Documentation

## A function to plot the original data along with the segments identified using segment of DNAcopy.

### Description

This function takes a DNAcopy object generated by running `getSegments` and then plots the original data along with the segments identified.

### Usage

    ## S3 method for class 'DNAcopy'
    plot(x, ..., save = FALSE, layout)

### Arguments

`x` | `x` is a DNAcopy object generated by `getSegments`
`...` | `...` may contain an optional boolean for save to indicate whether to show the plot on the screen (FALSE. Default) or return the name of the plot (TRUE) to allow the users to save the plot
`save` | `save` a boolean indicating wheather the plot will be draw on the screen only (FALSE) or the name of the png file of the plot be returned (TRUE)
`layout` | `layout` a numeric vector of two elements defining the values used for mfrow of the function par for the layout of figures on a plot

### Details

This function only works with the DNAcopy returned by `getSegments`. It will work with the DNAcopy returned by segment of the DNAcopy package when the a column containing the probe ids is added as the first column of the "data" element of the object.

### Value

This function returns invisible() or the name of the plot depending on whether save is set to FALSE of TRUE.

### Note

The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute

### Author(s)

Jianhua Zhang

### References

The DNAcopy package

### See Also

`getSegments`

### Examples

      if(interactive()){
        require("cghMCR")
        data("segData")
        plot(segData)
      }

[Package cghMCR version 1.40.0 Index]