md.plot: MD Plot
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Value Author(s) See Also Examples

Generates an MD plot for a specified value of Delta.

Contrary to a SAM plot in which the observed values of the test statistic D are plotted against the expected ones, the difference M between the observed and the expected values are plotted against the observed values in an MD plot.

  md.plot(object, delta, pos.stats = 1, sig.col = 3, xlim = NULL, ylim = NULL, 
        main = NULL, xlab = NULL, ylab = NULL, xsym = NULL, ysym = NULL, 
        forceDelta = FALSE, includeZero = TRUE, 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.
`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.
`xsym`	should the range of the plotted x-axis be symmetric about the origin? Ignored if `xlim` is specified. If `NULL`, `xsym` will be set to `TRUE`, if some of the observed values of the test statistic are negative. Otherwise, `xsym` will be set to `FALSE`.
`ysym`	should the range of the plotted y-axis be symmetric about the origin? Ignored if `ylim` is specified.If `NULL`, `ysym` will be set to `TRUE`, if some of the observed values of the test statistic are negative. Otherwise, `ysym` will be set to `FALSE`.
`forceDelta`	should the two horizontal lines at `delta` and -`delta` be within the plot region, no matter whether they are out of the range of the observed d values? Ignored if `ylim` is specified.
`includeZero`	should D = 0 and M = 0 be included in the plot, although all observed values of D (or M) are larger than zero?
`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 MD plot.

Holger Schwender, holger.schw@gmx.de

sam, sam.plot2

## 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
  plot(sam.out, 2)
  
  # As an alternative, the MD plot can be generated.
  md.plot(sam.out, 2)
  

## End(Not run)