MD Plot

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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

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  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

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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
  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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