R: SAM specific plot method (original) (raw)
| plot {siggenes} | R Documentation |
|---|
Description
Plots an object of class SAM. Generates either a SAM plot or a Delta plot
Usage
plot(x, y, 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, helplines = FALSE, ...)
Arguments
| x | an object of class SAM |
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| y | the delta value(s), i.e. either a numeric value or vector. If y is a numeric value, a SAM Plot for this delta value will be generated. If NULL or a vector, the Delta plots, i.e. a visualization of the table created by summary or print, are 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 y 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. By default, pos.stats=1 if the expression score d can be both positive and negative, and pos.stats=2 if d can only take positive values. Will be ignored when y is NULL or a vector |
| sig.col | a specification of the color of the significant genes. If sig.colhas 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. Will be ignored if y is NULL or a vector |
| xlim | a numeric vector of length 2 specifying the x limits (minimum and maximum) of the plot. Only used when y is a numeric value, i.e. when a SAM plot is generated |
| ylim | a numeric vector of length 2 specifying the y limits of the plot. Only used wheny is a numeric value |
| main | a character string naming the main title of the plot. Ignored if y is NULL or a vector |
| xlab | a character string naming the label of the x axis. Ignored if y is NULL or a vector |
| ylab | a character string naming the label of the y axis. Ignored if y is NULL or a vector |
| pty | a character specifying the type of plot region to be used. "s" (default) generates a square plotting region, and "m" the maximal plotting region. Ignored if y is NULL or a vector |
| 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. Ignored if y is NULL or a vector |
| 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. Ignored if y is NULL or a vector |
| sig.cex | a numerical value giving the amount by which the symbols of the significant genes should be scaled relative to the default. Ignored if y is NULL or a vector |
| helplines | logical specifying if help lines should be drawn into the Delta plots. Ignored ify is a numeric value |
| ... | further graphical parameters for the SAM plot. See ?plot.default and ?par. Ignored if y is NULL or a vector |
Value
a SAM plot or a Delta plot
Note
SAM was deveoped by Tusher et al. (2001).
!!! There is a patent pending for the SAM technology at Stanford University. !!!
Author(s)
Holger Schwender, holger.schw@gmx.de
References
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.
See Also
sam.plot2, delta.plot, sam, SAM-class
Examples
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
sam.plot2(sam.out,2)
Alternatively way of generating the same SAM plot
plot(sam.out,2)
Generate the Delta plots for the default set of Deltas computed by sam.
delta.plot(sam.out)
Another way of generating the same plot.
plot(sam.out)
Generate the Delta plots for Delta = 0.2, 0.4, ..., 2.
plot(sam.out,seq(0.2,2,0.2))