viewBeads {beadarray} | R Documentation |
View an image of the beads in a certain region, optionally with links between neighbours or certain beads highlighted.
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, ...)
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 . |
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.
Outputs to the active graphical device.
Jonathan Cairns
##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