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.