| plot {siggenes} | R Documentation |
Generates a plot of the posterior probabilities given by an object of class EBAM.
plot(x, y, pos.stats = 2, sig.col = 3, sig.cex = 1, pch = NULL, stats.cex = 0.8,
main = NULL, xlab = NULL, ylab = NULL, y.intersp = 1.3, ...)
x |
an object of class EBAM |
y |
the delta value, i.e. the minimum probability for a gene to be called differentially expressed |
pos.stats |
an integer between 0 and 4. If pos.stats=1, general
information as the number of significant genes and the estimated FDR for
the specified value of y will be plotted in the upper center of the
plot. If pos.stats=2, these information will be plotted in
the bottom right corner, if pos.stats=3 in the bottom left corner, and
if pos.stats=4 in the upper left corner. If pos.stats=0,
no information will be plotted |
sig.col |
a specification of the color of the significant genes.
For a description of how colors are specified, see the help of par |
sig.cex |
a numeric value giving the amount by which the symbols of the significant genes should be scaled relative to the default |
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
the help of par |
stats.cex |
the size of the statistics printed in the plot relative to the default size |
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 |
y.intersp |
a numeric value specifying the space between the rows in which the statistics are plotted |
... |
further graphical parameters for the EBAM plot. See the help pages of
plot.default and par |
a plot of the posterior probabilities of the genes for a specified value of
delta
Holger Schwender, [email protected]
Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.
Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.