plotArguments {siggenes}R Documentation

Plot Arguments

Description

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

Usage

  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)

Arguments

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

Value

a list required by sam2html or ebam2html if addPlot = TRUE

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

sam2html,ebam2html


[Package siggenes version 1.10.1 Index]