maanova (version 1.42.0)

arrayview: View the layout of input data

Description

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

By default, it will plot the log ratios for 2-dye array and raw intensity for 1-dye array. It does not work for N-dye (N>2) array at this time. Note that if user collapsed the replicates by using 'avgrep' in read.madata, and then arrayview will not be available.

Usage

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

Arguments

object

An object of class madata.

ratio

The data to be plotted. 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.

Examples

## Not run: 
# data(kidney)
# # arrayview 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)