sam.plot2: SAM Plot
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Value Author(s) References See Also Examples

Generates a SAM plot for a specified value of Delta.

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  sam.plot2(object, delta, pos.stats = NULL, sig.col = 3, xlim = NULL, 
        ylim = NULL, main = NULL, xlab = NULL, ylab = NULL, pty = "s", 
        lab = c(10, 10, 7), pch = NULL, sig.cex = 1, ...)

`object`	an object of class SAM.
`delta`	a numeric value specifying the value of Delta for which the SAM plot should be generated.
`pos.stats`	an integer between 0 and 2. If `pos.stats = 1`, general information as the number of significant genes and the estimated FDR for the specified value of `delta` will be plotted in the upper left corner of the plot. If `pos.stats = 2`, these information will be plotted in the lower right corner. If `pos.stats = 0`, no information will be plotted. By default, `pos.stats = 1` if the expression score d can be both positive and negative, and `pos.stats = 2` if d can only take positive values.
`sig.col`	a specification of the color of the significant genes. If `sig.col` has length 1, all the points corresponding to significant genes are marked in the color specified by `sig.col`. If `length(sig.col) == 2`, the down-regulated genes, i.e. the genes with negative expression score d, are marked in the color specified by `sig.col`[1], and the up-regulated genes, i.e. the genes with positive d, are marked in the color specified by `sig.col`[2]. For a description of how colors are specified, see `par`.
`xlim`	a numeric vector of length 2 specifying the x limits (minimum and maximum) of the plot.
`ylim`	a numeric vector of length 2 specifying the y limits of the plot.
`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.
`pty`	a character specifying the type of plot region to be used. `"s"` (default) generates a square plotting region, and `"m"` the maximal plotting region.
`lab`	a numeric vector of length 3 specifying the approximate number of tickmarks on the x axis and on the y axis and the label size.
`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 `par`.
`sig.cex`	a numerical value giving the amount by which the symbols of the significant genes should be scaled relative to the default.
`...`	further graphical parameters. See `plot.default` and `par`.

A SAM plot.

Holger Schwender, holger.schw@gmx.de

Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.

SAM-class,sam,md.plot

## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in multtest.
  library(multtest)
  data(golub)
  
  # Perform a SAM analysis for the two class unpaired case assuming
  # unequal variances.
  sam.out <- sam(golub, golub.cl, B=100, rand=123)
  
  # Generate a SAM plot for Delta = 2
  sam.plot2(sam.out, 2)
  
  # Alternatively way of generating the same SAM plot
  plot(sam.out, 2)
  
  # As an alternative, the MD plot can be generated.
  md.plot(sam.out, 2)
  

## End(Not run)