plotArguments: Plot Arguments
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Value Author(s) See Also

Utility function for generating a plot of a SAM or an EBAM object in an html output.

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  plotArguments(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, stats.cex = 0.8, y.intersp = 1.3)

`pos.stats`	an integer between 0 and 2 for a SAM plot, and between 0 and 4 for an EBAM plot. See `help.sam(plot)` or `help.ebam(plot)`, respectively, for how `pos.stats` can be specified, and for its default.
`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`. Only for a SAM plot: 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 for a SAM plot) generates a square plotting region, and `"m"` (default for an EBAM plot) 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.
`stats.cex`	the size of the statistics printed in the plot relative to the default size. Only available for an EBAM plot.
`y.intersp`	a numeric value specifying the space between the rows in which the statistics are plotted. Only available for an EBAM plot.