plotArguments {siggenes} | R Documentation |
Utility function for generating a plot of a SAM or an EBAM object in an html output.
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 |
a list required by sam2html
or ebam2html
if addPlot = TRUE
Holger Schwender, holger.schw@gmx.de