riplot {maanova} | R Documentation

## Ratio intensity plot for 2-dye Micro Array 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 both `rawdata` and `madata`. This function and `arrayview` assume the data field in `rawdata` is on the raw scale, and in `madata` is on log2 based scale. So if your rawdata is pre-transformed, you should not do riplot on the raw data.

### Usage

    riplot(object, title, 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` or `rawdata`.
`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.
`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.

### Note

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

### Author(s)

Hao Wu hao@jax.org

### Examples

    ## Not run:
    data(kidney)
    ############################
    # riplot on rawdata
    ############################
    # 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)

    ############################
    # RI plot on madata
    ############################
    data1 <- createData(kidney.raw)
    # do RI plot for all arrays
    riplot(data1)
    graphics.off()
    ## End(Not run)

[Package maanova version 0.98.8 Index]