plot: Visualize GSRI results
In GSRI: Gene Set Regulation Index

Description Usage Arguments Details Author(s) See Also Examples

Plot the empirical cumulative density along with the estimated degree of regulation of the p-value distribution for a gene set.

1	plot(x, y, ...)

`x`	An object of class `Gsri` containing the results to plot.
`y`	A single integer or character string specifying the results of which gene set to plot. This has to be given if `x` contains the results of several gene sets. An integer is interpreted as the index of the gene set (i.e. the row number), while a character is matched against the names of the gene sets.
`...`	Optional arguments used in order to customize the plot. See the ‘details’ section.

Plotting the p-value distribution and the estimation of the regularized compontent for a gene set allows to insepct the results in detail. The plot illustrates the empirical cumulative density function of the p-values obtained from testing for a differential effect between the groups. Additionally, the fit of the uniformly distributed component along with the estimated fraction of regularized genes and the GSRI is shown.

The plot method uses a special system in order to customize the graphical elements of the figure. It allows to refer to the different components with the name of the additional input argument; its value is a list containing named graphical parameters for the underlying plot function. The following list describes the possible names and their contribution.

plot: Arguments for the axis and the labeling, passed to the plot function.
fit: Arguments for the fit of the linear component of the ECDF, corresponding to the part without differential effect, passed to the lines function.
ecdf: Arguments for the ECDF of the p-values, passed to the lines function.
reg: Arguments for the horizontal line indicating the fraction of regulation, passed to the lines function.
regText: Arguments for the text label of reg, passed to the text function.
gsri: Arguments for the horizontal line indicating the GSRI, passed to the lines function.
gsriText: Arguments for the text label of gsri, passed to the text function.

Thus, changing for example the limit of the y-axis, the plot type and color of the ECDF, and the label of the x-axis, you can use:

plot(x, plot=list(ylim=c(0, 0.8), xlab=expression(p)), ecdf=list(type="s", col="darkgreen"))

For more details, please see the ‘examples’ section.

Julian Gehring

Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>

Package: GSRI-package

Class: Gsri

Methods: gsri getGsri getCdf getParms export sortGsri plot show summary readCls readGct

## Not run: 
plot(x)

plot(x, plot=list(main="Example plot"), ecdf=list(pch=21),
fit=list(lty=2, lwd=0.5, col="black"), gsri=list(col="lightblue"))

plot(x2, 2)
plot(x2, "gs2")

## End(Not run)