genefilter: rejection_plot – R documentation

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rejection_plot

Plot rejections vs. p-value cutoff

Description

Plot the number, or fraction, of null hypotheses rejected as a function of the p-value cutoff. Multiple sets of p-values are accepted, in a list or in the columns of a matrix, in order to permit comparisons.

Usage

rejection_plot(p,
               col, lty = 1, lwd = 1,   
               xlab = "p cutoff", ylab = "number of rejections",
               xlim = c(0, 1), ylim,
               legend = names(p),
               at = c("all", "sample"),
               n_at = 100,
               probability = FALSE,
               ...
               )

Arguments

`p`	The p-values to be used for plotting. These may be in the columns of a matrix, or in the elements of a list. One curve will be generated for each column/element, and all `NA` entries will be dropped. If column or element names are supplied, they are used by default for a plot legend.
`col`	Colors to be used for each curve plotted. Recycled if necessary. If `col` is omitted, `rainbow` is used to generate a set of colors.
`lty`	Line styles to be used for each curve plotted. Recycled if necessary.
`lwd`	Line widths to be used for each curve plotted. Recycled if necessary.
`xlab`	X-axis text label.
`ylab`	Y-axis text label.
`xlim`	X-axis limits.
`ylim`	Y-axis limits.
`legend`	Text for legend. Matrix column names or list element names (see `p` above) are used by default. If `NULL`, no legend is plotted.
`at`	Should step functions be plotted with a step at every value in `p`, or should linear interpolation be used at a sample of points spanning `xlim`? The latter looks when there are many p-values.
`n_at`	When `at = "sample"` is given, how many sample points should be used for interpolation and plotting?
`probability`	Should the fraction of null hypotheses rejected be reported instead of the count? See the `probability` argument to `hist`.
`...`	Other arguments to pass to the `plot` call which sets up the axes. Note that the `...` argument will not be passed to the `lines` calls which actually generate the curves.

Value

A list of the step functions used for plotting is returned invisibly.

Author(s)

Richard Bourgon <bourgon@ebi.ac.uk>

Examples

# See the vignette: Diagnostic plots for independent filtering

genefilter

genefilter: methods for filtering genes from high-throughput experiments

v1.72.1

Artistic-2.0

Authors

R. Gentleman, V. Carey, W. Huber, F. Hahne

Initial release