plotOnSAM {beadarray} | R Documentation

## Show variation between all 96 arrays

### Description

Function to show how quantities vary across all 96 arrays. eg mean intensity of a certain control probe

### Usage

    plotOnSAM(values, mx = max(values, na.rm = TRUE), scale = max(values,
    na.rm = TRUE), min = 0, main = NULL, label = TRUE, missing_arrays = NULL, colour=TRUE)

### Arguments

`values` | vector containing 96 numeric values to plot
`mx` | maximum value to display on y axis of plot
`scale` | numeric value giving the amount by which to divide all numbers by (eg for log2 intensities this should be 16) to transform to range 0 - 1
`min` | numeric value giving the minimum value to display on y axis
`main` | character string giving a title for the plot
`label` | boolean defining if the arrays are labeled on the plot
`missing_arrays` | vector of numeric values specifying the index of any arrays that have been removed from the SAM.
`colour` | if TRUE the hexagons will be plotted in colour

### Details

Two plots are produced side-by-side. The first is a plot of the set of values against the index 1-96 and secondly we plot 8 x 12 hexagonal arrays with array number 1 being the hexagon in the top-left corner and array 96 in the bottom-right. The colour of hexagon is directly related to the value in v for the particular array number. An array which has a higher value in v will be coloured brighter.

### Value

Plot is produced on current graphical device.

### Author(s)

Mark Dunning

[Package beadarray version 1.12.1 Index]