plot {siggenes} | R Documentation

## EBAM specific plot method

### Description

Generates a plot of the posterior probabilities given by an object of class EBAM.

### Usage

       plot(x, y, pos.stats = 2, sig.col = 3, sig.cex = 1, pch = NULL, stats.cex = 0.8,
            main = NULL, xlab = NULL, ylab = NULL, y.intersp = 1.3, ...)

### Arguments

`x` | an object of class EBAM
`y` | the delta value, i.e. the minimum probability for a gene to be called differentially expressed

`pos.stats`

an integer between 0 and 4. If `pos.stats=1`, general information as the number of significant genes and the estimated FDR for the specified value of `y` will be plotted in the upper center of the plot. If `pos.stats=2`, these information will be plotted in the bottom right corner, if `pos.stats=3` in the bottom left corner, and if `pos.stats=4` in the upper left corner. If `pos.stats=0`, no information will be plotted

`sig.col` | a specification of the color of the significant genes. For a description of how colors are specified, see the help of `par`
`sig.cex` | a numeric value giving the amount by which the symbols of the significant genes should be scaled relative to the default
`pch` | either an integer specifying a symbol or a single character to be used as the default in plotting points. For a description of how `pch` can be specified, see the help of `par`
`stats.cex` | the size of the statistics printed in the plot relative to the default size
`main` | a character string naming the main title of the plot
`xlab` | a character string naming the label of the x axis
`ylab` | a character string naming the label of the y axis
`y.intersp` | a numeric value specifying the space between the rows in which the statistics are plotted
`...` | further graphical parameters for the EBAM plot. See the help pages of `plot.default` and `par`

### Value

a plot of the posterior probabilities of the genes for a specified value of `delta`

### Author(s)

Holger Schwender, holger.schw@gmx.de

### References

Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.

Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.