plot {siggenes} | R Documentation |

Plots an object of class SAM. Generates either a SAM plot or a Delta plot

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, ...)

`x` |
an object of class SAM |

`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.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` . 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 when
`y` 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 if
`y` is a numeric value |

`...` |
further graphical parameters for the SAM plot. See `?plot.default` and
`?par` . Ignored if `y` is NULL or a vector |

a SAM plot or a Delta plot

SAM was deveoped by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!

Holger Schwender, holger.schw@gmx.de

Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays
applied to the ionizing radiation response. *PNAS*, 98, 5116-5121.

`sam.plot2`

, `delta.plot`

, `sam`

, `SAM-class`

## 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)) ## End(Not run)