md.plot {siggenes} | R Documentation |
Generates an MD plot for a specified value of Delta.
Contrary to a SAM plot in which the observed values of the test statistic D are plotted against the expected ones, the difference M between the observed and the expected values are plotted against the observed values in an MD plot.
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, ...)
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. |
... |
further graphical parameters. See plot.default and
par . |
A MD plot.
Holger Schwender, holger.schw@gmx.de
## Not run: # Load the package multtest and the data of Golub et al. (1999) # contained in multtest. library(multtest) data(golub) # Perform a SAM analysis for the two class unpaired case assuming # unequal variances. sam.out <- sam(golub, golub.cl, B=100, rand=123) # Generate a SAM plot for Delta = 2 plot(sam.out, 2) # As an alternative, the MD plot can be generated. md.plot(sam.out, 2) ## End(Not run)