maanova (version 1.42.0)

riplot: Ratio intensity plot for 2-dye Microarray experiment

Description

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.

Usage

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

Arguments

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.

Examples

## 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)