plot.twilight {twilight}R Documentation

A plot function for twilight objects

Description

Interface to plotting of twilight objects. Produces one of five possible plots.

Usage

plot.twilight(x, which = "fdr", grayscale = FALSE, legend = TRUE, ...)

Arguments

x An object of class twilight.
which A character string specifying the plot to be made.
grayscale Logical value. Specifying whether plots should be colored or grayscaled. Only necessary for "scores" and "fdr".
legend Logical value. Produces a legend for "scores" and "effectsize". A legend for "fdr" is only available if bootstrap estimates exist.
... Additional graphical arguments.

Details

Option which="scores" plots the expected versus the observed test statistics and draws confidence lines calculated from permutations. This plot is similar to plots in Tusher et al. (2001).

Option which="qvalues" plots q-values versus the number of rejected hypotheses.

Option which="fdr" plots p-values versus 1 - local false discovery rate, that is the conditional probability of being significant given the corresponding p-value, plus bootstrap estimates if computed. Bottom ticks are 1%-quantiles of p-values.

Option which="volcano" results in the volcano plot, that is observed score versus 1 - local false discovery rate. Bottom ticks are 1%-quantiles of scores.

Option which="effectsize" plots the observed fold change equivalent score distribution overlaid by the estimated effect size distribution, that is distribution of scores under the alternative. This plot is only available if function twilight.pval was applied with method="fc" as fold change equivalent scores are computed from log ratios.

Option which="table" tabulates histogram "effectsize".

Value

No value is returned except for "table".

Author(s)

Stefanie Scheid http://www.molgen.mpg.de/~scheid

References

Scheid S and Spang R (2004): A stochastic downhill search algorithm for estimating the local false discovery rate, IEEE TCBB 1(3), 98–108.

Tusher VG, Tibshirani R and Chu G (2001): Significance analysis of mircroarrays applied to the ionizing response, PNAS 98(9), 5116–5121.

See Also

twilight.pval, twilight

Examples

data(exfdr) # contains a twilight object created by twilight
plot(exfdr,which="fdr")

[Package twilight version 1.4.0 Index]