plotBeadLocations {beadarray}R Documentation

Show bead locations

Description

Shows location of a set of beads on an array. The beads can either be defined to be all beads with particular ProbeIDs or individual beadIDs

Usage

plotBeadLocations(BLData, ProbeIDs=NULL, BeadIDs=NULL, array, SAM=FALSE,...)

Arguments

BLData a BeadLevelList object
ProbeIDs a vector of ProbeIDs to plot
BeadIDs a vector of beadIDs to plot
array numeric value specifying the array
SAM if TRUE then the data is assumed to be taken from a SAM array and therefore hexagonal
... further graphical parameters to plot

Details

The outline of the hexagonal array is drawn and the locations of the specified beads are overlayed.

Value

Plot is produced on the current graphical device.

Author(s)

Mark Dunning

Examples


data(BLData)

#plot all beads with ProbeID 2 on array 1
plotBeadLocations(BLData, ProbeIDs=2, array=1)

#plot all beads with either ProbeID 2 or 10

plotBeadLocations(BLData, ProbeIDs=c(2, 10), array=1)

#can also change plotting characters

plotBeadLocations(BLData, ProbeIDs=c(2, 10), array=1, col="red", pch="X", cex=2)

#find all outliers on the first array and plot their locations
o=findAllOutliers(BLData, 1)

plotBeadLocations(BLData, beadIDs=o, array=1)



[Package beadarray version 1.2.2 Index]