md.plot {siggenes} | R Documentation

## MD Plot

### Description

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.

### Usage

      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, ...)

### 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.
`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`.

### Value

A MD plot.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### See Also

`sam`, `sam.plot2`

### 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
      plot(sam.out, 2)

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

    ## End(Not run)

[Package siggenes version 1.68.0 Index]