sam.plot2 {siggenes} | R Documentation

## SAM Plot

### Description

Generates a SAM plot for a specified value of Delta.

### Usage

      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

    ## 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)

[Package siggenes version 1.64.0 Index]