SAM Plot

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Description

Generates a SAM plot for a specified value of Delta.

Usage

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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, ...)

Arguments

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.

Value

A SAM plot.

Author(s)

Holger Schwender, holger.schw@gmx.de

References

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

See Also

SAM-class,sam,md.plot

Examples

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## 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)

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