viewBeads {beadarray}R Documentation

View Beads

Description

View an image of the beads in a certain region, optionally with links between neighbours or certain beads highlighted.

Usage

viewBeads(BLData, array, x, y, xwidth = 100, ywidth = 100, neighbours = NULL, mark = NULL, markcol = "blue", markpch = 21, inten = TRUE, low = "black", high = "green", what = "G", log = TRUE, zlim = NULL, ...)

Arguments

BLData BeadLevelList
array integer specifying which strip/array to plot
x numeric value - x co-ordinate to centre on
y numeric value - y co-ordinate to centre on
xwidth numeric value - width of square
ywidth numeric value - width of square
neighbours Neighbours matrix (optional) - if specified, links will be drawn between neighbours. (See generateNeighbours.)
mark integral vector (optional) - a list of beadIDs to highlight.
markcol The colour used for the highlighted beads.
markpch The colour used for the highlighted beads.
inten logical - if true, plot coloured circles, with shades corresponding to intensities. Intensities are retrieved using getArrayData, and the arguments below.
low Colour used for low intensities.
high Colour used for high intensities.
what Data to be used - passed to getArrayData.
log Data to be used - passed to getArrayData.
zlim Limits to be used. Supply in form c(0,5).
... Additional arguments passed to getArrayData.

Details

viewBeads plots the beads within the defined square region.

Specifying a neighbours matrix will result in links between neighbours being plotted. Specifying a mark vector of beadIDs will result in the beads with these beadIDs being highlighted with a blue circular border.

Value

Outputs to the active graphical device.

Author(s)

Jonathan Cairns

See Also

generateNeighbours

Examples

##data(BLData)
##o <- findAllOutliers(BLData,2)

##x11()
##viewBeads(BLData, 2, 1000,1200,250,250, mark = o) ## outliers in this ##region are marked in blue
##x11()
##viewBeads(BLData, 2, 1000,1200,250,250, mark = o, inten = FALSE) ## ##removing the intensities makes the outlier locations easier to see

##neighbours <- generateNeighbours(BLData, 2)
##x11()
##viewBeads(BLData, 2, 1000,1200,250,250, neighbours) ## observe that ##there are many missing beads in this region, affecting the neighbours ##algorithm

[Package beadarray version 1.10.0 Index]