riplot: Ratio intensity plot for 2-dye Microarray experiment
In maanova: Tools for analyzing Micro Array experiments

Description Usage Arguments Note Author(s) Examples

This function only works for 2-dye array at this time. It will plot the log-ratio (log2(R/G)) versus log-intensity (log2(R*G)/2) figure for Micro Array experiment. Ideal RI plot will be points scattered around the y=0 horizontal line.

This function works for madata. This function and arrayview assume the data is on log2 based scale. So if your rawdata is not pre-transformed, you should not do riplot on the raw data.

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riplot(object, title, xlab, ylab, array, color = "blue",highlight.flag = TRUE, 
    flag.color = "Red", idx.highlight, highlight.color = "Green", 
    rep.connect = FALSE, onScreen=TRUE)

`object`	An object of class `madata`.
`title`	The title for figures. The default figure title is "RI plot for array number X". If the user wants to provide titles, be sure to provide a string array with the same number of elements as the number of arrays.
`xlab`	The xlab for figures. The default figure xlab is "expression(log[2](R*G))". One xlab would be used for all plot, thus unlike title, user (if one wants) need to provide only one name.
`ylab`	The ylab for figures. The default figure ylab is "expression(log[2](R/G))". One ylab would be used for all plot, thus unlike title, user (if one wants) need to provide only one name.
`array`	A list of arrays numbers for which you want to draw an RI plot.
`color`	The color for the points in scatter plot. Default is blue.
`highlight.flag`	A logical parameter to indicate whether to highlight the bad spots or not.
`flag.color`	The color for bad spots, default is red.
`idx.highlight`	A vector for highlighted spots other than bad spots.
`highlight.color`	The color for highlighted spots. Default is green.
`rep.connect`	A logical value to represent whether to connect the dots between the replicates or not.
`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.

This function will plot one figure for each array. So if you have many arrays, there will be many figures generated.

Hao Wu

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

## End(Not run)