boxplotBeads {beadarray} | R Documentation

## Box plot of bead intensities

### Description

Function to produce box plots of the bead intensities from selected strips/arrays from a `BeadLevelList` object.

### Usage

    boxplotBeads(BLData, whatToPlot = "G", arrays = NULL, log = TRUE,
              varwidth = TRUE, method = "illumina", n = 3, trim = 0.05, ...)

### Arguments

`BLData` | `BeadLevelList`
`whatToPlot` | character string specifying which intensities to plot. See `getArrayData` for a list of the possibilities.
`arrays` | integer (scalar or vector) specifying the strips/arrays to plot. If `NULL`, all the strips/arrays are plotted.
`log` | if TRUE log2 intensities are plotted
`varwidth` | logical, indicating whether box widths should be proportional to the number of values in each box plot
`method` | character string specifying the summarisation method to use (only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`). Refer to help `createBeadSummaryData` help page for further information.
`n` | numeric value defining a cut-off for the number of median absolute deviations (MADs) from the median to use for determining outliers. The default value is 3. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"` and `method="illumina"`. Refer to help `createBeadSummaryData` help page for further information.
`trim` | fraction of intensities to remove from the bead summary calculations. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to `createBeadSummaryData` help page for further information.
`...` | further graphical parameters to the `boxplot` function from the graphics package

### Details

Produces box plots of the specified intensities for selected strips/arrays.

### Value

A plot is produced on the current graphical device

### Author(s)

Matt Ritchie

### Examples

    data(BLData)

    boxplotBeads(BLData)

[Package beadarray version 1.12.1 Index]