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.