plotRG {beadarray} | R Documentation

## Plot bead level data: R vs G intensities

### Description

Shows R and G intensities fom a BeadLevelList object. The beads can either be defined to be all beads with particular ProbeIDs or rows BeadIDs

### Usage

    plotRG(BLData, ProbeIDs=NULL, BeadIDs=NULL, log=TRUE, arrays=1,
                       xlim=c(8,16), ylim=c(8,16), xlab="G intensities",
                       ylab="R intensities",
                       main=arrayNames(BLData)[arrays], smooth=TRUE,
                       cols=NULL, ...)

### Arguments

`BLData` | a BeadLevelList object
`ProbeIDs` | a vector of ProbeIDs to plot
`BeadIDs` | logical/integer vector specifying which rows of data to plot (used if ProbeIDs is NULL)
`log` | logical, if TRUE, take log base 2 of intensities
`arrays` | which array/s to plot
`xlim` | x-axis limits for plot
`ylim` | y-axis limits for plot
`xlab` | character string specifying x-axis label
`ylab` | character string specifying y-axis label
`main` | main plot title
`smooth` | logical, whether to smooth the points (only used when one array is selected for plotting)
`cols` | colours to use on the plot
`...` | further graphical parameters to `plot`

### Details

The R and G intensities from selected beads and arrays are plotted.

### Value

Plot is produced on the current graphical device.

### Author(s)

Matt Ritchie

### Examples

    data(BLData)

    #plot all beads from array 1
    plotRG(BLData, arrays=1)

    #plot Beads with ProbeIDs 2 on arrays 1-4
    plotRG(BLData, arrays=1:4, ProbeIDs=1000, pch=16)

[Package beadarray version 1.4.0 Index]