arrayview {maanova} | R Documentation

## View the layout of input data

### Description

This function reconstructs the input data according to the micro array grid location structure and plots the data according to the user specified color map.

Dy default, it will plot the log ratios for 2-dye array and raw intensity for 1-dye array. It doesnot work for N-dye (N>2) array at this time.

Note that if user collapsed the replicates in creating the `madata` object (see `createData`), arrayview will be unavailable.

### Usage

    arrayview(object, ratio, array, colormap, onScreen=TRUE, ...)

### Arguments

`object` | An object of class `madata` or `rawdata`.
`ratio` | The data to be ploted. The length of it must be equal to the length of the grid locations, .e.g, madata$row and madata$col. If ratio is a vector, there will be one plot. If ratio is a matrix, there will be one plot for each column. If ratio is not provided, `link[maanova]{make.ratio}` will be called to calculate the ratios from the original data.
`array` | A list of arrays to be plotted. This variable is only valid when `ratio` is not provided. Whenever `ratio` is provided, all columns in ratio will be plotted.
`colormap` | User specified color map. See `colors` for more detail.
`...` | Other parameters to be passed to `image`.
`onScreen` | A logical value to represent whether to display the plots on screen or not. If TRUE, x11() (in Unix/Windows) or macintosh (in Mac) will be called inside the function. Otherwise, it will plot the figure on the current device. Default is TRUE.

### Author(s)

Hao Wu

### Examples

    ## Not run:
    data(kidney)
    ############################
    # arrayview plot on rawdata
    ############################
    # arrayview raw data on screen
    arrayview(kidney.raw, array=1)
    graphics.off()
    # arrayview raw data array 1 and 3 and output to postscript file
    postscript(file="kidneyArrayview.ps")
    arrayview(kidney.raw, array=c(1,3), onScreen=FALSE)
    ## End(Not run)

    # once the replicates are collapsed,
    # arrayview will be unavailable
    ## Not run: data1 <- createData(kidney.raw, n.rep=2, avgreps=1)
    ## Not run: arrayview(data1) # get an error here

[Package maanova version 1.6.0 Index]