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 1.12.1 Index]