GSRI (version 2.20.0)

plot-methods: Visualize GSRI results

Description

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

Usage

plot(x, y, ...)

Arguments

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.

Details

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.

See Also

Package: GSRI-package Class: Gsri Methods: gsri getGsri getCdf getParms export sortGsri plot show summary readCls readGct

Examples

## 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)