interactivePlots {beadarray} | R Documentation

## Interactive bead level plotting

### Description

Plots using bead level data to discover spatial effects and artifacts on arrays

### Usage

    SAMSummary(BLData, mode = "outliers", whatToPlot = "G", log = TRUE,
                   n = 3, missing_arrays = NULL, colour = TRUE,
                   scale = NULL, low = "yellow", high="red", ...)
    BeadChipSummary(BLData, mode = "outliers", whatToPlot = "G", log = TRUE,
                   n = 3, colour = TRUE, scale = NULL, low = "yellow",
                   high = "red", ...)

### Arguments

`BLData` | BeadLevelList object
`mode` | character string either "outliers" or "intensities" specifying what to display on the plots
`whatToPlot` | character string specifying which intensities to plot. Possibilities are `"G"`, `"Gb"` for single channel data and `"G"`, `"Gb"`, `"R"` and `"Rb"` for two-colour data
`log` | if TRUE log2 intensities of each bead are used to find outliers
`n` | Specify a cut-off for outliers as n median absolute deviations from the median. The default value is 3
`missing_arrays` | vector of numeric values specifying the index of any arrays that have been removed from the SAM.
`colour` | if TRUE the hexagons will be plotted in colour
`scale` | numeric value giving the amount by which to divide all numbers by (eg for log2 intensities this should be 16) to transform to range 0 - 1
`low` | Color for area of lowest intensity
`high` | color for area of highest intensity
`...` | other graphical parameters to plot that can be specified

### Details

A plot will be displayed giving a summary of each array in the experiment on the left screen and initially a blank right hand side. The left hand side is coloured according to the number of outliers found on the array or the mean intensity of the array (depending on the mode parameter). Clicking on tha particular array on the left will display a location plot of the outliers or an image plot on the right See RNews article

### Value

Plot will be produced on the current graphical device

### Author(s)

Mark Dunning

[Package beadarray version 1.4.0 Index]