interactivePlots {beadarray} | R Documentation

## Interactive bead-level plotting

### Description

Generates spatial plots using bead-level data to discover artefacts on strips/arrays.

### Usage

    SAMSummary(BLData, mode = "outliers", whatToPlot = "G",  samID = NULL,
                   log = TRUE, n = 3, colour = TRUE,
                   scale = NULL, low = "yellow", high="red", ...)
    BeadChipSummary(BLData, mode = "outliers", whatToPlot = "G", chipID = NULL,
                   stripsPerChip = 12, 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
`samID` | character string specifying which SAM to plot. If `NULL`, data from the first SAM is plotted.
`chipID` | character string specifying which BeadChip to plot. If `NULL`, data from the first BeadChip is plotted.
`stripsPerChip` | integer specifying number of strips on BeadChip (8 or 12)
`log` | if TRUE log2 intensities of each bead are used to find outliers
`n` | numeric value specifying the number of median absolute deviations (MADs) from the median to use as a cut-off for outliers. The default value is 3
`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` | colour to use for lowest intensity
`high` | colour to use for highest intensity
`...` | other parameters to `imageplot` 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

A plot is produced on the current graphical device

### Author(s)

Mark Dunning

[Package beadarray version 1.12.1 Index]