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Last data update: 2014.03.03

R: A function to plot the original data along with the segments...

plot.DNAcopy

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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cghMCR)
Loading required package: DNAcopy
Loading required package: CNTools
Loading required package: tools
Loading required package: genefilter
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cghMCR/plot.DNAcopy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.DNAcopy
> ### Title: A function to plot the original data along with the segments
> ###   identified using segment of DNAcopy.
> ### Aliases: plot.DNAcopy
> ### Keywords: hplot
> 
> ### ** Examples
> 
> #  if(interactive()){
>     require("cghMCR")
>     data("segData")
>     plot(segData)
Error in xy.coords(x, y) : argument "min" is missing, with no default
Calls: plot ... plot.DNAcopy -> <Anonymous> -> polygon -> xy.coords
Execution halted