| riplot {maanova} | R Documentation |
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.
riplot(object, title, 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 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. |
This function will plot one figure for each array. So if you have many arrays, there will be many figures generated.
Hao Wu hao@jax.org
## 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)