plotBeadLocations {beadarray}R Documentation

Plot bead locations

Description

Shows location of a set of beads on a strip/array. The beads can either be defined to be all beads with particular ProbeIDs or as rows in BeadLevelList.

Usage

plotBeadLocations(BLData, ProbeIDs = NULL, BeadIDs = NULL, array = 1,
                   SAM = FALSE, xlab = "x-coordinate",
                   ylab = "y-coordinate",
                   main = paste("Bead", ProbeIDs,"locations"), ...)

Arguments

BLData BeadLevelList
ProbeIDs a vector of ProbeIDs to plot
BeadIDs logical/integer vector specifying which rows of data from BeadLevelList) to plot (used if ProbeIDs is NULL)
array integer specifying the strip/array to plot
SAM if TRUE then the data is assumed to be taken from a SAM array and therefore hexagonal
xlab character string specifying x-axis label
ylab character string specifying y-axis label
main character string specifying plot title
... further graphical parameters to plot

Details

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

Value

A 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, array=1, ProbeIDs=2, SAM=TRUE)

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

[Package beadarray version 1.10.0 Index]