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 1.10.0 Index]